Changes between Version 31 and Version 32 of SOPs/rna-seq-diff-expressions

Timestamp:

08/11/16 12:52:21 (8 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -30 +30 @@
     * Typically we use [[http://www-huber.embl.de/users/anders/HTSeq/doc/count.html|htseq-count]] to get counts for each gene
       * 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.
+      * 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).
       * 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.