Question: filtering pair-end bam file
0
npetr • 0 wrote:
Hello, I am trying to filter a pairend bam file to get only forward reads in Galaxy. A bam filter from bamtools does not seem do exactly what I mean, in fact it seems that it filters both read 1 and read 2 but I would like to only have read 1 filtered in order to obtain only fragments mapped to forward strand. Could you please suggest a correct way to do this?
Hey, thank you very much for your reply Jen, so do you mean this filtering result in Pair End bam file containing only pairs where read 1 is mapped to forward strand? best Natalia
This filters to leave reads that are mapped to the forward strand. These are not necessarily the first read in a properly paired mapped pair.