Mercurial > repos > iuc > trinity_samples_qccheck

changeset 20:04bb8bb7c198 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:11:17 +0000
parents 1b1a25f93f80
children
files samples_qccheck.xml test-data/count/contig_exn50_statistic/Trinity.fasta.gz test-data/count/trinityStats/statsfile.txt
diffstat 3 files changed, 41 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/samples_qccheck.xml	Tue Apr 11 19:49:25 2023 +0000
+++ b/samples_qccheck.xml	Tue Aug 08 09:11:17 2023 +0000
@@ -89,7 +89,7 @@
 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
 
 
-.. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
 ]]>
     </help>
 
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinityStats/statsfile.txt	Tue Aug 08 09:11:17 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
+
+
+