Dear QuasR developers,
I would like to use the qAlign function in QuasR. However, I do not see any parameters for specifying the number of mismatches allowed (-v parameter in bowtie) or the number of alignments (-k parameter in bowtie) to output for a multi-mapping read. According to the help menu, a single alignment is randomly selected in case of a multi-mapping read.
Could you please let me know whether it is possible to specify v and k in qAlign? Would you suggest I should use Rbowtie::bowtie instead.
Best regards, Julie