Mercurial > repos > iuc > deseq2
changeset 20:89d26b11d452 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
| author | iuc |
|---|---|
| date | Thu, 06 Dec 2018 15:49:22 -0500 |
| parents | c56e0689e46e |
| children | a6fc9228e1a0 |
| files | deseq2.xml get_deseq_dataset.R test-data/Homo_sapiens.GRCh38.94.gtf test-data/out_deseq2_sailfish.tab test-data/sailfish_ensembl/sailfish_quant.sf1.tab test-data/sailfish_ensembl/sailfish_quant.sf2.tab test-data/sailfish_ensembl/sailfish_quant.sf3.tab test-data/sailfish_ensembl/sailfish_quant.sf4.tab test-data/sailfish_ensembl/sailfish_quant.sf5.tab test-data/sailfish_ensembl/sailfish_quant.sf6.tab |
| diffstat | 10 files changed, 306 insertions(+), 9 deletions(-) [+] |
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--- a/deseq2.xml Tue Dec 04 08:19:06 2018 -0500 +++ b/deseq2.xml Thu Dec 06 15:49:22 2018 -0500 @@ -348,7 +348,7 @@ </assert_contents> </output> </test> - <!--Ensure Sailfish/Salmon input with GFF3 annotation works--> + <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works--> <test expect_num_outputs="1"> <repeat name="rep_factorName"> <param name="factorName" value="Treatment"/> @@ -372,6 +372,30 @@ </assert_contents> </output> </test> + <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works--> + <test expect_num_outputs="1"> + <repeat name="rep_factorName"> + <param name="factorName" value="Treatment"/> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> + </repeat> + </repeat> + <param name="pdf" value="False"/> + <param name="tximport_selector" value="tximport"/> + <param name="txtype" value="sailfish"/> + <param name="mapping_format_selector" value="gtf"/> + <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> + <output name="deseq_out" > + <assert_contents> + <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark
--- a/get_deseq_dataset.R Tue Dec 04 08:19:06 2018 -0500 +++ b/get_deseq_dataset.R Thu Dec 06 15:49:22 2018 -0500 @@ -57,13 +57,16 @@ }) txdb <- makeTxDbFromGFF(gffFile) k <- keys(txdb, keytype = "TXNAME") - tx2gene <- select(txdb, k, "GENEID", "TXNAME") + tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME") + # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name) + tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME) } try(txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene)) if (!exists("txi")) { - # Remove version from transcript IDs - tx2gene$TXNAME <- sub('\\.[0-9]+', '', tx2gene$TXNAME) - txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene) + # Remove version from transcript IDs in tx2gene... + tx2gene$TXNAME <- sub('\\.[0-9]+$', '', tx2gene$TXNAME) + # ...and in txiFiles + txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene, ignoreTxVersion=TRUE) } dds <- DESeqDataSetFromTximport(txi, subset(sampleTable, select=-c(filename)),
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Homo_sapiens.GRCh38.94.gtf Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,178 @@ +#!genome-build GRCh38.p12 +#!genome-version GRCh38 +#!genome-date 2013-12 +#!genome-build-accession NCBI:GCA_000001405.27 +#!genebuild-last-updated 2018-07 +# Trimmed version of ftp://ftp.ensembl.org/pub/release-94/gtf/homo_sapiens/Homo_sapiens.GRCh38.94.gtf.gz +5 ensembl_havana gene 36035017 36071358 . - . gene_id "ENSG00000168671"; gene_version "9"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +5 ensembl_havana transcript 36035017 36066891 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana exon 36066696 36066891 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; exon_id "ENSE00001299572"; exon_version "2"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana CDS 36066696 36066789 . - 0 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; protein_id "ENSP00000282507"; protein_version "3"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana start_codon 36066787 36066789 . - 0 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana exon 36064249 36064350 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "2"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; exon_id "ENSE00003574795"; exon_version "1"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana CDS 36064249 36064350 . - 2 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "2"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; protein_id "ENSP00000282507"; protein_version "3"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana exon 36051870 36051984 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "3"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; exon_id "ENSE00003558123"; exon_version "1"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana CDS 36051870 36051984 . - 2 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "3"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; protein_id "ENSP00000282507"; protein_version "3"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana exon 36048889 36049420 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "4"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; exon_id "ENSE00001122183"; exon_version "1"; tag "basic"; transcript_support_level "1"; +5 ensembl_havana CDS 36048889 36049420 . - 1 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000282507"; transcript_version "7"; exon_number "4"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS3914"; 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transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana exon 36066696 36066882 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003618618"; exon_version "1"; transcript_support_level "2"; +5 havana CDS 36066696 36066789 . - 0 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; protein_id "ENSP00000426017"; protein_version "1"; transcript_support_level "2"; +5 havana start_codon 36066787 36066789 . - 0 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "1"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana exon 36064249 36064350 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "2"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003574795"; exon_version "1"; transcript_support_level "2"; +5 havana CDS 36064249 36064350 . - 2 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "2"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; protein_id "ENSP00000426017"; protein_version "1"; transcript_support_level "2"; +5 havana exon 36051870 36051984 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "3"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003558123"; exon_version "1"; transcript_support_level "2"; +5 havana CDS 36051870 36051984 . - 2 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "3"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; protein_id "ENSP00000426017"; protein_version "1"; transcript_support_level "2"; +5 havana exon 36039477 36039708 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "4"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003578191"; exon_version "1"; transcript_support_level "2"; +5 havana CDS 36039660 36039708 . - 1 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "4"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; protein_id "ENSP00000426017"; protein_version "1"; transcript_support_level "2"; +5 havana stop_codon 36039657 36039659 . - 0 gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "4"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana exon 36037797 36038016 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "5"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003691910"; exon_version "1"; transcript_support_level "2"; +5 havana exon 36035355 36035974 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; exon_number "6"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; exon_id "ENSE00003625951"; exon_version "1"; transcript_support_level "2"; +5 havana five_prime_utr 36066790 36066882 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana three_prime_utr 36039477 36039656 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana three_prime_utr 36037797 36038016 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +5 havana three_prime_utr 36035355 36035974 . - . gene_id "ENSG00000168671"; gene_version "9"; transcript_id "ENST00000504685"; transcript_version "5"; gene_name "UGT3A2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "UGT3A2-202"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; transcript_support_level "2"; +12 ensembl_havana gene 53938765 53946544 . + . gene_id "ENSG00000123364"; gene_version "4"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 53938765 53946544 . + . gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53938765 53939642 . + . gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "1"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; exon_id "ENSE00000838327"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53938907 53939642 . + 0 gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "1"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; protein_id "ENSP00000243056"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 53938907 53938909 . + 0 gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "1"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53945000 53946544 . + . gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "2"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; exon_id "ENSE00000838328"; exon_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53945000 53945253 . + 2 gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "2"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; protein_id "ENSP00000243056"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 53945254 53945256 . + 0 gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; exon_number "2"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 53938765 53938906 . + . gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 53945257 53946544 . + . gene_id "ENSG00000123364"; gene_version "4"; transcript_id "ENST00000243056"; transcript_version "4"; gene_name "HOXC13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8865"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 53954834 53958956 . + . gene_id "ENSG00000123407"; gene_version "3"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 53954834 53958956 . + . gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53954834 53955539 . + . gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "1"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; exon_id "ENSE00001059266"; exon_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53954930 53955539 . + 0 gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "1"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; protein_id "ENSP00000243103"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 53954930 53954932 . + 0 gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "1"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53956328 53958956 . + . gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "2"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; exon_id "ENSE00000838329"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53956328 53956563 . + 2 gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "2"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; protein_id "ENSP00000243103"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 53956564 53956566 . + 0 gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; exon_number "2"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 53954834 53954929 . + . gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 53956567 53958956 . + . gene_id "ENSG00000123407"; gene_version "3"; transcript_id "ENST00000243103"; transcript_version "3"; gene_name "HOXC12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8866"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 53973126 53977643 . + . gene_id "ENSG00000123388"; gene_version "4"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 53973126 53977643 . + . gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53973126 53973923 . + . gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; exon_id "ENSE00002343306"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53973242 53973923 . + 0 gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; protein_id "ENSP00000446680"; protein_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 53973242 53973244 . + 0 gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53975181 53977643 . + . gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "2"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; exon_id "ENSE00002362919"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53975181 53975410 . + 2 gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "2"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; protein_id "ENSP00000446680"; protein_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 53975411 53975413 . + 0 gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; exon_number "2"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 53973126 53973241 . + . gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 53975414 53977643 . + . gene_id "ENSG00000123388"; gene_version "4"; transcript_id "ENST00000546378"; transcript_version "1"; gene_name "HOXC11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8867"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 53985065 53990279 . + . gene_id "ENSG00000180818"; gene_version "4"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 53985186 53990279 . + . gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53985186 53986010 . + . gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "1"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; exon_id "ENSE00001151648"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53985260 53986010 . + 0 gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "1"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; protein_id "ENSP00000307321"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 53985260 53985262 . + 0 gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "1"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 53989169 53990279 . + . gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "2"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; exon_id "ENSE00001151643"; exon_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 53989169 53989443 . + 2 gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "2"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; protein_id "ENSP00000307321"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 53989444 53989446 . + 0 gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; exon_number "2"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 53985186 53985259 . + . gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 53989447 53990279 . + . gene_id "ENSG00000180818"; gene_version "4"; transcript_id "ENST00000303460"; transcript_version "4"; gene_name "HOXC10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8868"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 53990624 54030823 . + . gene_id "ENSG00000197757"; gene_version "7"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 54015897 54030733 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54015897 54017414 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "1"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; exon_id "ENSE00002068738"; exon_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54028576 54028921 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; exon_id "ENSE00001518112"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54028768 54028921 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; protein_id "ENSP00000377864"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54028768 54028770 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54029655 54030733 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; exon_id "ENSE00002030800"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54029655 54029959 . + 2 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; protein_id "ENSP00000377864"; protein_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54029960 54029962 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; exon_number "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54015897 54017414 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54028576 54028767 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54029963 54030733 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000394331"; transcript_version "3"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS41792"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana transcript 54028358 54030823 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54028358 54028921 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "1"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; exon_id "ENSE00000838340"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54028522 54028921 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "1"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; protein_id "ENSP00000243108"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54028522 54028524 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "1"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54029655 54030823 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; exon_id "ENSE00000838341"; exon_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54029655 54029959 . + 2 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; protein_id "ENSP00000243108"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54029960 54029962 . + 0 gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; exon_number "2"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54028358 54028521 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54029963 54030823 . + . gene_id "ENSG00000197757"; gene_version "7"; transcript_id "ENST00000243108"; transcript_version "4"; gene_name "HOXC6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC6-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8871"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 53994895 54003337 . + . gene_id "ENSG00000180806"; gene_version "4"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 54000119 54003337 . + . gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54000119 54000726 . + . gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "1"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; exon_id "ENSE00001151635"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54000189 54000726 . + 0 gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "1"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; protein_id "ENSP00000302836"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54000189 54000191 . + 0 gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "1"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54002430 54003337 . + . gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "2"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; exon_id "ENSE00001151626"; exon_version "5"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54002430 54002671 . + 2 gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "2"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; protein_id "ENSP00000302836"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54002672 54002674 . + 0 gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; exon_number "2"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54000119 54000188 . + . gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54002675 54003337 . + . gene_id "ENSG00000180806"; gene_version "4"; transcript_id "ENST00000303450"; transcript_version "4"; gene_name "HOXC9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8869"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 54009106 54012362 . + . gene_id "ENSG00000037965"; gene_version "5"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 54009106 54012362 . + . gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54009106 54009720 . + . gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "1"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; exon_id "ENSE00000748009"; exon_version "6"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54009285 54009720 . + 0 gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "1"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; protein_id "ENSP00000040584"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54009285 54009287 . + 0 gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "1"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54011089 54012362 . + . gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "2"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; exon_id "ENSE00000838338"; exon_version "6"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54011089 54011378 . + 2 gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "2"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; protein_id "ENSP00000040584"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54011379 54011381 . + 0 gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; exon_number "2"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54009106 54009284 . + . gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54011382 54012362 . + . gene_id "ENSG00000037965"; gene_version "5"; transcript_id "ENST00000040584"; transcript_version "5"; gene_name "HOXC8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8870"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 54016931 54056030 . + . gene_id "ENSG00000198353"; gene_version "7"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 54016931 54055327 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54016931 54017414 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "1"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00002087480"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54053160 54053276 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00001518109"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54053917 54054361 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "3"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00001151579"; exon_version "5"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54053923 54054361 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "3"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; protein_id "ENSP00000305973"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54053923 54053925 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "3"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54054850 54055327 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00001661316"; exon_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54054850 54055202 . + 2 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; protein_id "ENSP00000305973"; protein_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54055203 54055205 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; exon_number "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54016931 54017414 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54053160 54053276 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54053917 54053922 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54055206 54055327 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000303406"; transcript_version "4"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana transcript 54053877 54056030 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana exon 54053877 54054361 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "1"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00001664549"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 havana CDS 54053923 54054361 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "1"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; protein_id "ENSP00000399808"; protein_version "2"; tag "basic"; transcript_support_level "1"; +12 havana start_codon 54053923 54053925 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "1"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana exon 54054850 54056030 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; exon_id "ENSE00001257489"; exon_version "5"; tag "basic"; transcript_support_level "1"; +12 havana CDS 54054850 54055202 . + 2 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; protein_id "ENSP00000399808"; protein_version "2"; tag "basic"; transcript_support_level "1"; +12 havana stop_codon 54055203 54055205 . + 0 gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; exon_number "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana five_prime_utr 54053877 54053922 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana three_prime_utr 54055206 54056030 . + . gene_id "ENSG00000198353"; gene_version "7"; transcript_id "ENST00000430889"; transcript_version "2"; gene_name "HOXC4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8873"; tag "basic"; transcript_support_level "1"; +12 havana gene 54017110 54035361 . + . gene_id "ENSG00000273046"; gene_version "1"; gene_name "HOXC5"; gene_source "havana"; gene_biotype "processed_transcript"; +12 havana transcript 54017110 54035361 . + . gene_id "ENSG00000273046"; gene_version "1"; transcript_id "ENST00000512206"; transcript_version "1"; gene_name "HOXC5"; gene_source "havana"; gene_biotype "processed_transcript"; transcript_name "HOXC5-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1"; +12 havana exon 54017110 54017414 . + . gene_id "ENSG00000273046"; gene_version "1"; transcript_id "ENST00000512206"; transcript_version "1"; exon_number "1"; gene_name "HOXC5"; gene_source "havana"; gene_biotype "processed_transcript"; transcript_name "HOXC5-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002024343"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 havana exon 54034278 54035361 . + . gene_id "ENSG00000273046"; gene_version "1"; transcript_id "ENST00000512206"; transcript_version "1"; exon_number "2"; gene_name "HOXC5"; gene_source "havana"; gene_biotype "processed_transcript"; transcript_name "HOXC5-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00001190306"; exon_version "3"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana gene 54032853 54035358 . + . gene_id "ENSG00000172789"; gene_version "3"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; +12 ensembl_havana transcript 54032853 54035358 . + . gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54032853 54033576 . + . gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "1"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; exon_id "ENSE00001190317"; exon_version "4"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54033123 54033576 . + 0 gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "1"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; protein_id "ENSP00000309336"; protein_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana start_codon 54033123 54033125 . + 0 gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "1"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana exon 54034278 54035358 . + . gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; exon_id "ENSE00002053096"; exon_version "1"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana CDS 54034278 54034489 . + 2 gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; protein_id "ENSP00000309336"; protein_version "2"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana stop_codon 54034490 54034492 . + 0 gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; exon_number "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana five_prime_utr 54032853 54033122 . + . gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; tag "basic"; transcript_support_level "1"; +12 ensembl_havana three_prime_utr 54034493 54035358 . + . gene_id "ENSG00000172789"; gene_version "3"; transcript_id "ENST00000312492"; transcript_version "2"; gene_name "HOXC5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "HOXC5-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS8872"; tag "basic"; transcript_support_level "1";
--- a/test-data/out_deseq2_sailfish.tab Tue Dec 04 08:19:06 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -MIR6859-2 1.1858265336986 -1.58325519934585 1.29566733255222 -1.22196119294536 0.221722302676964 0.886889210707857 -DDX11L1 1.91972630671259 -0.204757212641591 1.31524142129485 -0.155680325548148 0.876285006005361 0.999999999763967 -MIR6859-1 0.294068009390125 -0.712896459907293 1.28824575367762 -0.55338545294805 0.579999497913718 0.999999999763967 -WASH7P 114.545909292233 -3.75034693001422e-10 1.2677635335979 -2.95823852841924e-10 0.999999999763967 0.999999999763967
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf1.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1759.2 0 0 +ENST00000546378.1 2035 1837.2 0 0 +ENST00000243103.3 847 649.348 0 0 +ENST00000243056.4 2395 2555.05 0.0173509 1 +ENST00000303406.4 2305 2261.56 0.114436 5.83783 +ENST00000430889.2 1665 1561.63 3.55316 125.162 +ENST00000312492.2 1610 1412.2 0 0 +ENST00000512206.1 1644 1446.2 0 0 +ENST00000243108.4 1680 1482.2 0 0 +ENST00000394331.3 2077 1879.2 0 0 +ENST00000040584.5 2286 2088.2 0 0 +ENST00000303450.4 1539 1341.2 0 0 +ENST00000513300.5 2281 2071 0.085625 4 +ENST00000282507.7 2383 2153.11 0 0 +ENST00000504685.5 1851 1659.15 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf2.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1764.64 0 0 +ENST00000546378.1 2035 2171.69 0.0161522 1 +ENST00000243103.3 847 655.215 0 0 +ENST00000243056.4 2395 2567.91 0.01366 1 +ENST00000303406.4 2305 2235.74 0 0 +ENST00000430889.2 1665 1576.16 1.7359 78 +ENST00000312492.2 1610 1726.1 1.31761e-06 6.48367e-05 +ENST00000512206.1 1644 1704.36 0.0411608 1.99994 +ENST00000243108.4 1680 1679.47 0.10443 5 +ENST00000394331.3 2077 2069.83 0 0 +ENST00000040584.5 2286 2093.64 0 0 +ENST00000303450.4 1539 1557.46 0.0675669 3 +ENST00000513300.5 2281 2088.64 0 0 +ENST00000282507.7 2383 2190.64 0 0 +ENST00000504685.5 1851 1658.64 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf3.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1760.44 0 0 +ENST00000546378.1 2035 2127.85 0.0280759 2 +ENST00000243103.3 847 650.573 0 0 +ENST00000243056.4 2395 2198.44 0 0 +ENST00000303406.4 2305 2223.92 0.0661957 4.92838 +ENST00000430889.2 1665 1536.71 2.08127 107.072 +ENST00000312492.2 1610 1685.74 1.23894e-08 6.99193e-07 +ENST00000512206.1 1644 1658.72 0.0720329 4 +ENST00000243108.4 1680 1638.79 0.0546819 3 +ENST00000394331.3 2077 2026.99 0 0 +ENST00000040584.5 2286 2089.44 0 0 +ENST00000303450.4 1539 1342.44 0 0 +ENST00000513300.5 2281 2047.58 0 0 +ENST00000282507.7 2383 2143.36 0 0 +ENST00000504685.5 1851 1659.97 0.0359895 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf4.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1738.38 0 0 +ENST00000546378.1 2035 1816.38 0 0 +ENST00000243103.3 847 628.444 0 0 +ENST00000243056.4 2395 2176.38 0 0 +ENST00000303406.4 2305 2086.38 0 0 +ENST00000430889.2 1665 1510.43 2.31417 89.0334 +ENST00000312492.2 1610 1391.38 0 0 +ENST00000512206.1 1644 1425.38 0 0 +ENST00000243108.4 1680 1612.63 0.0730348 3 +ENST00000394331.3 2077 1998.27 0 0 +ENST00000040584.5 2286 2067.38 0 0 +ENST00000303450.4 1539 1320.38 0 0 +ENST00000513300.5 2281 2033.58 0 0 +ENST00000282507.7 2383 2129.01 0 0 +ENST00000504685.5 1851 1639.11 0.071855 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf5.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1781.23 0 0 +ENST00000546378.1 2035 1859.23 0 0 +ENST00000243103.3 847 671.305 0 0 +ENST00000243056.4 2395 2219.23 0 0 +ENST00000303406.4 2305 2195.37 0 0 +ENST00000430889.2 1665 1545.8 3.39643 119.002 +ENST00000312492.2 1610 1715.91 0.128558 5 +ENST00000512206.1 1644 1468.23 0 0 +ENST00000243108.4 1680 1654.16 0.0800141 3 +ENST00000394331.3 2077 2034.63 0 0 +ENST00000040584.5 2286 2148.18 0.0205378 1 +ENST00000303450.4 1539 1363.23 0 0 +ENST00000513300.5 2281 2061.52 0 0 +ENST00000282507.7 2383 2156.64 0 0 +ENST00000504685.5 1851 1671.47 0.0527904 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_ensembl/sailfish_quant.sf6.tab Thu Dec 06 15:49:22 2018 -0500 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +ENST00000303460.4 1957 1747.9 0 0 +ENST00000546378.1 2035 1825.9 0 0 +ENST00000243103.3 847 638.159 0 0 +ENST00000243056.4 2395 2562.99 0.0171188 1 +ENST00000303406.4 2305 2272.12 0.152979 7.92213 +ENST00000430889.2 1665 1572.52 3.54659 127.112 +ENST00000312492.2 1610 1731.28 0.0760279 3 +ENST00000512206.1 1644 1434.9 0 0 +ENST00000243108.4 1680 1673.79 0.104853 4 +ENST00000394331.3 2077 2057.73 0 0 +ENST00000040584.5 2286 2185.1 0.0200793 1 +ENST00000303450.4 1539 1329.9 0 0 +ENST00000513300.5 2281 2047.55 0 0 +ENST00000282507.7 2383 2143.62 0 0 +ENST00000504685.5 1851 1663.05 0.0263825 1