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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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A question about -X #389

Closed NJU-Bio-Info closed 1 year ago

NJU-Bio-Info commented 2 years ago

Hi, when I use bowtie2 to perform CUT&Tag alignment. I set -X 700 and filter the reads whose mapq<20 but I can still observe fragment size >700 in bam file. I wonder why I get this result?

ch4rr0 commented 1 year ago

I was able to reproduce this issue. I will update this thread as soon as I have a proper fix.

ch4rr0 commented 1 year ago

Taking a second look at the issue it appears that some of your reads are longer than the 700 nucleotides you specified for maxIns. bowtie2 then adjusts the value of maxIns by setting it to the length of the longer fragment that makes up the pair. So I ask, what is your scenario and what behavior were you looking for?

BenLangmead commented 1 year ago

(Just following on @ch4rr0's comment, since he and I discussed this earlier.) We're curious: Does it make sense to you that some of the reads produced by the CUT&Tag assay would be quite long, longer even than what you specified for the -X parameter?