Mercurial > repos > iuc > trinity_define_clusters_by_cutting_tree
changeset 19:65e7dea767ea 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 09:06:08 +0000 |
| parents | ae501908a17f |
| children | |
| files | define_clusters_by_cutting_tree.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/define_clusters_by_cutting_tree.xml Tue Apr 11 19:50:15 2023 +0000 +++ b/define_clusters_by_cutting_tree.xml Tue Aug 08 09:06:08 2023 +0000 @@ -81,7 +81,7 @@ This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool. -.. _Trinity: http://trinityrnaseq.github.io +.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki ]]> </help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinityStats/statsfile.txt Tue Aug 08 09:06:08 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 + + +