Good day,
Now I know about invertStrand, I agree that it's best to keep the strandMode
only for paired-end data. Indeed, it's an example at the end of the lengthy
documentation of GAlignments.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
On 01/13/2017 12:36 PM, Hervé Pagès wrote:
Hi,
No ifelse() statement needed. Just use invertStrand() on your
GAlignments object to invert its strand.
strandMode is specific to paired-end reads and the supported modes
reflect what other software do with paired-end reads (e.g. TopHat,
Rsubread,
Good day,
readGAlignmentPairs has strandMode but readGAlignments doesn't, which means
that single-end strand-specific RNA-seq that generates sequences on the
opposite strand to the gene needs a subsequent ifelse statement. The API could
be more consistent by providing a strandMode option for
