Changes between Version 8 and Version 9 of SOPs/rna-seq-diff-expressions_TE

Timestamp:

02/25/21 10:23:11 (4 years ago)

Author:

twhitfie

Comment:

--

SOPs/rna-seq-diff-expressions_TE

@@ -38 +38 @@
 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
 }}}
-    * The design for tests of differential expression above is a comparison between to 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.
+    * 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.
     * The output from TEtranscripts includes tests of differential expression carried out using [http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html DESeq2], in addition to a (sample x transcript) matrix of counts.
  * **Alternative software**