Changes between Version 30 and Version 31 of SOPs/rna-seq-diff-expressions

Timestamp:

06/01/16 10:46:28 (9 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -34 +34 @@
       * Counting can be also performed transcript level but this may be too much information.
       * htseq-count can accept SAM or BAM (-f option), for example
-         * ''htseq-count -f bam -m intersection-strict --stranded=reverse accepted_hits.sortedByName.bam gene_models.gtf >| gene_model.counts.txt''
+         * ''htseq-count -f bam -m intersection-strict --stranded=reverse MySample.accepted_hits.sortedByName.bam gene_models.gtf >| MySample.counts.txt''
          * Note that htseq-count assumes that your reads are strand-specific; default is --stranded=yes
          * If your reads are not stranded, use "--stranded=no" (or half of your reads won't be counted).  If they're stranded and in the opposite direction from the transcript, use "--stranded=reverse".