| Next changeset 1:9f80c71f1779 (2015-03-05) |
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Commit message:
Imported from capsule None |
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added:
stringtie.xml test-data/._stringtie_in1.bam test-data/._stringtie_out2.gtf test-data/stringtie_in1.bam test-data/stringtie_out1.gtf test-data/stringtie_out2.gtf tool_dependencies.xml |
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| diff -r 000000000000 -r 62d212192002 stringtie.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stringtie.xml Thu Jul 03 18:38:02 2014 -0400 |
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| @@ -0,0 +1,117 @@ +<?xml version="1.0"?> +<tool name="StringTie" id="stringtie" version="1.0.0"> + <description>RNA-Seq assembler</description> + <requirements> + <requirement type="package" version="0.97">stringtie</requirement> + </requirements> + <command> +<![CDATA[ +stringtie "$input_bam" +-o "$output_gtf" +-p "\${GALAXY_SLOTS:-1}" +#if str($guide.use_guide) == 'yes': + -G "$guide.guide_gff" $guide.input_estimation + -C "$coverage" +#end if +#if str($option_set.options) == 'advanced': + -f "$option_set.fraction" + -m "$option_set.min_tlen" + -a "$option_set.min_anchor_len" + -j "$option_set.min_anchor_cov" + -c "$option_set.min_bundle_cov" + -s "$option_set.maxcov" + -g "$option_set.bdist" + -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming +#end if +]]> +</command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file to assemble" /> + <conditional name="guide"> + <param name="use_guide" type="select" label="Use GFF file to guide assembly"> + <option value="yes">Use GFF</option> + <option value="no" selected="True">Do not use GFF</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" /> + <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" /> + </when> + </conditional> + <conditional name="option_set"> + <param name="options" type="select" label="Options"> + <option value="default" selected="True">Use defaults</option> + <option value="advanced">Specify advanced options</option> + </param> + <when value="default" /> + <when value="advanced"> + <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" /> + <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" /> + <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" /> + <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" /> + <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" /> + <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" /> + <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" /> + <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" /> + <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" /> + <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" /> + <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/> + <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage"> + <filter>guide['use_guide'] == "yes"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_bam" value="stringtie_in1.bam" ftype="bam" /> + <param name="use_guide" value="no" /> + <param name="options" value="default" /> + <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" /> + </test> + <test> + <param name="input_bam" value="stringtie_in1.bam" ftype="bam" /> + <param name="use_guide" value="no" /> + <param name="options" value="advanced" /> + <param name="fraction" value="0.17" /> + <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" /> + </test> + </tests> + <help> +<![CDATA[ +StringTie v0.97 usage:: + + stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>] + [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens] + [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>] + + Assemble RNA-Seq alignments into potential transcripts. + + Options: + -G reference annotation to use for guiding the assembly process (GTF/GFF3) + -l name prefix for output transcripts (default: STRG) + -f minimum isoform fraction (default: 0.15) + -m minimum assembled transcript length to report (default 200bp) + -o output file with the assembled transcripts (default: stdout) + -a minimum anchor length for junctions (default: 10) + -j minimum junction coverage (default: 1) + -t disable trimming of predicted transcripts based on coverage (default: trimming enabled) + -c minimum bundle reads per bp coverage to consider for assembly (default: 2) + -s coverage saturation threshold; further read alignments will be + ignored in a region where a local coverage depth of <maxcov> + is reached (default: 1,000,000); + -v verbose (log bundle processing details) + -e abundance estimation only of input transcripts (for -G option) + -g gap between read mappings triggering a new bundle (default: 50) + -S more sensitive run (default: no) + -C output file with all transcripts in reference that are fully + covered by reads + -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) + -p number of threads (CPUs) to use (default: 1) + +]]> +</help> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 62d212192002 test-data/stringtie_in1.bam |
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| Binary file test-data/stringtie_in1.bam has changed |
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| diff -r 000000000000 -r 62d212192002 test-data/stringtie_out1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out1.gtf Thu Jul 03 18:38:02 2014 -0400 |
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| b'@@ -0,0 +1,154 @@\n+chr19\tStringTie\ttranscript\t3052907\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";\n+chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";\n+chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";\n+chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";\n+chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";\n+chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";\n+chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";\n+chr19\tStringTie\texon\t3062172\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";\n+chr19\tStringTie\ttranscript\t3052907\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";\n+chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";\n+chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";\n+chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";\n+chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";\n+chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";\n+chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";\n+chr19\tStringTie\texon\t3062698\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";\n+chr19\tStringTie\ttranscript\t2997664\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";\n+chr19\tStringTie\texon\t2997664\t2997953\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";\n+chr19\tStringTie\texon\t3000645\t3000721\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";\n+chr19\tStringTie\texon\t3002351\t3002501\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";\n+chr19\tStringTie\texon\t3005435\t3005582\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";\n+chr19\tStringTie\texon\t3005719\t3005966\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";\n+chr19\tStringTie\texon\t3006418\t3006667\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";\n+chr19\tStringTie\texon\t3008867\t3008943\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";\n+chr19\tStringTie\texon\t3009540\t3009700\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";\n+chr19\tStringTie\texon\t3011020\t3011158\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";\n+chr19\tStringTie\texon\t3013667\t3013816\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";\n+chr19\tStringTie\texon\t3014568\t3014612\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";\n+chr19\tStringTie\texon\t3015651\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";\n+chr19\tStringTie\ttranscript\t3018960\t3029141\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";\n+chr19\tStringTie\texon\t3018960\t3019461\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";\n+chr19\tStringTie\texon\t3019697\t3019771\t100'..b'"71.914742";\n+chr19\tStringTie\texon\t3453761\t3453914\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "9"; cov "30.357872";\n+chr19\tStringTie\texon\t3456548\t3456633\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "10"; cov "40.561024";\n+chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "11"; cov "74.051750";\n+chr19\tStringTie\ttranscript\t3366538\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; cov "18.338432";FPKM "3938.679688";\n+chr19\tStringTie\texon\t3366538\t3366664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";\n+chr19\tStringTie\texon\t3381710\t3382241\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";\n+chr19\tStringTie\texon\t3425104\t3425175\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";\n+chr19\tStringTie\texon\t3433516\t3433590\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";\n+chr19\tStringTie\texon\t3434275\t3434398\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";\n+chr19\tStringTie\texon\t3435081\t3435205\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";\n+chr19\tStringTie\texon\t3449012\t3449137\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";\n+chr19\tStringTie\texon\t3452480\t3452664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";\n+chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";\n+chr19\tStringTie\ttranscript\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";\n+chr19\tStringTie\texon\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";\n+chr19\tStringTie\ttranscript\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";\n+chr19\tStringTie\texon\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";\n+chr19\tStringTie\ttranscript\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";\n+chr19\tStringTie\texon\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";\n+chr19\tStringTie\ttranscript\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";\n+chr19\tStringTie\texon\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";\n+chr19\tStringTie\ttranscript\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";\n+chr19\tStringTie\texon\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";\n+chr19\tStringTie\ttranscript\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";\n+chr19\tStringTie\texon\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";\n+chr19\tStringTie\ttranscript\t3490820\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";\n+chr19\tStringTie\texon\t3490820\t3491809\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";\n+chr19\tStringTie\texon\t3492260\t3492497\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";\n+chr19\tStringTie\texon\t3494026\t3494102\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";\n+chr19\tStringTie\texon\t3496539\t3496884\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";\n+chr19\tStringTie\texon\t3500559\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";\n' |
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| diff -r 000000000000 -r 62d212192002 test-data/stringtie_out2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out2.gtf Thu Jul 03 18:38:02 2014 -0400 |
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| b'@@ -0,0 +1,145 @@\n+chr19\tStringTie\ttranscript\t3052907\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";\n+chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";\n+chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";\n+chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";\n+chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";\n+chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";\n+chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";\n+chr19\tStringTie\texon\t3062172\t3062360\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";\n+chr19\tStringTie\ttranscript\t3052907\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";\n+chr19\tStringTie\texon\t3052907\t3054038\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";\n+chr19\tStringTie\texon\t3054118\t3054192\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";\n+chr19\tStringTie\texon\t3055662\t3055724\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";\n+chr19\tStringTie\texon\t3056310\t3056354\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";\n+chr19\tStringTie\texon\t3057677\t3057740\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";\n+chr19\tStringTie\texon\t3061158\t3061255\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";\n+chr19\tStringTie\texon\t3062698\t3063089\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";\n+chr19\tStringTie\ttranscript\t2997664\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";\n+chr19\tStringTie\texon\t2997664\t2997953\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";\n+chr19\tStringTie\texon\t3000645\t3000721\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";\n+chr19\tStringTie\texon\t3002351\t3002501\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";\n+chr19\tStringTie\texon\t3005435\t3005582\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";\n+chr19\tStringTie\texon\t3005719\t3005966\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";\n+chr19\tStringTie\texon\t3006418\t3006667\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";\n+chr19\tStringTie\texon\t3008867\t3008943\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";\n+chr19\tStringTie\texon\t3009540\t3009700\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";\n+chr19\tStringTie\texon\t3011020\t3011158\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";\n+chr19\tStringTie\texon\t3013667\t3013816\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";\n+chr19\tStringTie\texon\t3014568\t3014612\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";\n+chr19\tStringTie\texon\t3015651\t3015854\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";\n+chr19\tStringTie\ttranscript\t3018960\t3029141\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";\n+chr19\tStringTie\texon\t3018960\t3019461\t1000\t-\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";\n+chr19\tStringTie\texon\t3019697\t3019771\t100'..b'"71.914742";\n+chr19\tStringTie\texon\t3453761\t3453914\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "9"; cov "30.357872";\n+chr19\tStringTie\texon\t3456548\t3456633\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "10"; cov "40.561024";\n+chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "11"; cov "74.051750";\n+chr19\tStringTie\ttranscript\t3366538\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; cov "18.338432";FPKM "3938.679688";\n+chr19\tStringTie\texon\t3366538\t3366664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";\n+chr19\tStringTie\texon\t3381710\t3382241\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";\n+chr19\tStringTie\texon\t3425104\t3425175\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";\n+chr19\tStringTie\texon\t3433516\t3433590\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";\n+chr19\tStringTie\texon\t3434275\t3434398\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";\n+chr19\tStringTie\texon\t3435081\t3435205\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";\n+chr19\tStringTie\texon\t3449012\t3449137\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";\n+chr19\tStringTie\texon\t3452480\t3452664\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";\n+chr19\tStringTie\texon\t3462750\t3469274\t1000\t+\t.\tgene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";\n+chr19\tStringTie\ttranscript\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";\n+chr19\tStringTie\texon\t3472911\t3473297\t1000\t.\t.\tgene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";\n+chr19\tStringTie\ttranscript\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";\n+chr19\tStringTie\texon\t3473383\t3473585\t1000\t.\t.\tgene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";\n+chr19\tStringTie\ttranscript\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";\n+chr19\tStringTie\texon\t3473881\t3474130\t1000\t.\t.\tgene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";\n+chr19\tStringTie\ttranscript\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";\n+chr19\tStringTie\texon\t3474201\t3474891\t1000\t.\t.\tgene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";\n+chr19\tStringTie\ttranscript\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";\n+chr19\tStringTie\texon\t3475786\t3476529\t1000\t.\t.\tgene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";\n+chr19\tStringTie\ttranscript\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";\n+chr19\tStringTie\texon\t3474957\t3475188\t1000\t-\t.\tgene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";\n+chr19\tStringTie\ttranscript\t3490820\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";\n+chr19\tStringTie\texon\t3490820\t3491809\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";\n+chr19\tStringTie\texon\t3492260\t3492497\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";\n+chr19\tStringTie\texon\t3494026\t3494102\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";\n+chr19\tStringTie\texon\t3496539\t3496884\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";\n+chr19\tStringTie\texon\t3500559\t3500661\t1000\t-\t.\tgene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";\n' |
| b |
| diff -r 000000000000 -r 62d212192002 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 03 18:38:02 2014 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="stringtie" version="0.97"> + <repository changeset_revision="bbcdfb50d3f0" name="package_stringtie_0_97" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |