Bowtie2 --strata problem

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.

bowtie2 strata

• 2,538 views • link

updated 5.8 years ago by Antonio Camargo

• written 10.8 years ago by Avi Srivastava

Filtering according to the AS tag should work. Can you elaborate on why that didn't work for you?

• 0 views • link

updated 6.7 years ago by Ram

• written 10.8 years ago by Devon Ryan

0 answers

No answers yet.

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