Changes between Version 11 and Version 12 of SOPs/rna-seq-diff-expressions_TE

Timestamp:

10/30/25 15:45:34 (4 days ago)

Author:

kdesilva

Comment:

--

SOPs/rna-seq-diff-expressions_TE

@@ -36 +36 @@
 {{{
 # Reverse stranded reads
-bsub TEtranscripts --format BAM --stranded reverse -t /path/to/treat1.bam /path/to/treat2.bam -c /path/to/control1.bam /path/to/control2.bam --GTF /path/to/gene.gtf --TE /path/to/TE.gtf --mode multi --project treat_vs_control --minread 1 -i 100 --padj 0.05 --norm DESeq_default --sortByPos
+sbatch --job-name=TEtranscripts --mem=32G --wrap="TEtranscripts --format BAM --stranded reverse -t /path/to/treat1.bam /path/to/treat2.bam -c /path/to/control1.bam /path/to/control2.bam --GTF /path/to/gene.gtf --TE /path/to/TE.gtf --mode multi --project treat_vs_control --minread 1 -i 100 --padj 0.05 --norm DESeq_default --sortByPos"
 }}}
     * The design for tests of differential expression above is a comparison between two biological contexts (e.g. treatment versus control, samples listed after the -t flag versus samples listed after the -c flag).  If your experimental design is more complex, you should use TEcounts with a subsequent custom analysis of differential expression.