Currently xFASTQ allows analyzing unstranded libraries only (meaning that even possible stranded libraries are analyzed as unstranded).
In particular, even if the --readStrand option was mistakenly included in 2.7.0a,b releases, STAR does not utilize library strandedness information for mapping (see this STAR issue).
On the contrary, RSEM has an easy basic option for this:
--strandedness <none|forward|reverse>
with the recommendation of using reverse for Illumina TruSeq Stranded protocols (as per the userguide here).
...so, it should be easy to add an option to anqFASTQ to select the correct RSEM's strandedness value.
Currently xFASTQ allows analyzing unstranded libraries only (meaning that even possible stranded libraries are analyzed as unstranded).
In particular, even if the
--readStrandoption was mistakenly included in 2.7.0a,b releases, STAR does not utilize library strandedness information for mapping (see this STAR issue).On the contrary, RSEM has an easy basic option for this:
with the recommendation of using
reversefor Illumina TruSeq Stranded protocols (as per the userguide here)....so, it should be easy to add an option to anqFASTQ to select the correct RSEM's strandedness value.