Changes between Version 41 and Version 42 of SOPs/rna-seq-diff-expressions

Timestamp:

05/17/17 10:55:39 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -59 +59 @@
       * Sample commands:
 {{{
+#default: unstranded
 #single-end reads
 featureCounts -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
 #PE reads
 featureCounts -p -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
+
+#stranded (fwd)
+featureCounts -p -s 1 -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
+
 }}}
     * For some analyses (or for visualization), you can add a pseudocount (such as 1 or another small number) to all genes in all samples to prevent log2 ratios that require dividing by 0 and reduce background count noise -- BUT be aware that some statistical methods (like DESeq) require raw input values without any pseudocounts or normalization.