How to remove specifically non aligned regions

Question

[curiousbiologist]

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!

Answer 1

[Brice Sarver]

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