How to remove specifically non aligned regions
Hi all,
I would like to select a specific region from a fastq file (all read matching this region) and if they exceed the reference, trim only the non matching regions. I've done a bwa alignment and generated sam file but I'm not sure how remove the regions that are not matching to the reference without removing all the read
Thanks for your help!
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Brice Sarver
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curiousbiologist •
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curiousbiologist •
1 answer
You'll want to subset the BAM based on the region you want. This can be done easily with samtools.
Check out this Biostars post: Extract Reads From A Bam File That Fall Within A Given Region
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