Entering edit mode
8.5 years ago
Avi Srivastava
▴
130
Does anybody have any idea about how to extract from Bowtie 2's output (when run with -k), an equivalent to Bowtie1's best stratum.
or is there alternative in which i can filter bowtie2's result to get "equally best" alignments only in the top stratum(best scored) alignments. I've tried MAPQ field and optional tags like AS and XS but it didn't worked out.
Thanks.
Filtering according to the AS tag should work. Can you elaborate on why that didn't work for you?