Changes between Version 51 and Version 52 of SOPs/rna-seq-diff-expressions

Timestamp:

06/29/17 10:56:32 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -31 +31 @@
       * Include same GTF file describing gene models as was used for mapping -- but think carefully about what genes should be included (such as long non-coding RNAs, microRNAs, or piRNAs)
       * Is your sequencing library stranded or unstranded?  This information is needed to help htseq-count accurately count features.  If the library prep method is "TruSeqStrandedPolyA", for example, the reads will be stranded in the reverse direction (relative to the transcript orientation).
+        * See [[SAMBAMqc]] to determine strandedness
       * Carefully choose the best "mode" to handle reads that don't completely map to exactly one gene.
       * Counting can be also performed transcript level but this may be too much information.
@@ -62 +63 @@
 # single-end reads (unstranded)
 featureCounts -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
+# single-end reads (forward stranded)
+featureCounts -s 1 -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
+# single-end reads (reverse stranded)
+featureCounts -s 2 -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam
+
 
 # paired-end reads (unstranded)