Mercurial > repos > iuc > trinity_contig_exn50_statistic
changeset 16:870ac06dff8e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
| author | iuc |
|---|---|
| date | Tue, 08 Aug 2023 09:08:40 +0000 |
| parents | 41db7569b4ba |
| children | |
| files | contig_exn50_statistic.xml test-data/count/contig_exn50_statistic/Trinity.fasta.gz test-data/count/trinityStats/statsfile.txt |
| diffstat | 3 files changed, 41 insertions(+), 1 deletions(-) [+] |
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--- a/contig_exn50_statistic.xml Tue Apr 11 19:48:34 2023 +0000 +++ b/contig_exn50_statistic.xml Tue Aug 08 09:08:40 2023 +0000 @@ -35,7 +35,7 @@ It takes as input a transcriptome assembled with Trinity and the matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. -.. _Trinity: http://trinityrnaseq.github.io +.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki ]]> </help> <expand macro="citation" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinityStats/statsfile.txt Tue Aug 08 09:08:40 2023 +0000 @@ -0,0 +1,40 @@ + + +################################ +## Counts of transcripts, etc. +################################ +Total trinity 'genes': 7 +Total trinity transcripts: 7 +Percent GC: 42.12 + +######################################## +Stats based on ALL transcript contigs: +######################################## + + Contig N10: 541 + Contig N20: 541 + Contig N30: 380 + Contig N40: 380 + Contig N50: 279 + + Median contig length: 240 + Average contig: 298.14 + Total assembled bases: 2087 + + +##################################################### +## Stats based on ONLY LONGEST ISOFORM per 'GENE': +##################################################### + + Contig N10: 541 + Contig N20: 541 + Contig N30: 380 + Contig N40: 380 + Contig N50: 279 + + Median contig length: 240 + Average contig: 298.14 + Total assembled bases: 2087 + + +