Mapped to reverse strand read

[raqsilva]

Hi all,

I have noticed that when calculating the "mapped reads nucleotide content" reads are not reverse complemented. I used qualimap_v2.2.1, ran Picard CollectBaseDistributionByCycle and pysam to see the differences. If I don't reverse complement reads on pysam the output will be the same as qualimap.

As we can see from the images below the N content should only have one peak at the end of read 2 and should be around 25%, which is expected from a swath failure.

Hope I made myself clear! Best regards

[Konstantin Okonechnikov]

Hi! Thanks a lot for the report! Indeed the strand was not controlled when collecting base pair information, this won't have the impact to collect general GC-content or polymers, but influences the plot. Please check the version with the fix: https://bitbucket.org/kokonech/qualimap/downloads/qualimap-build-28-08-17.tar.gz