How to only keep read that cover a certain region
Hi, I have aligned ONT data with minimap2 with hg19 as reference.
Now I want to keep only the read that cover entirely a certain region.
I search certain tool like bedtools but didn't find the proper parameter. Any idea how to do that ?
Thanks
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nbargues •
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samtools view. Provide a BED file of the region co-ordinates you are interested in.It seems to work but I have zero read as output.
I try also this :
bedtools intersect -wa -F 1 -a FAN46998_minimap2_ont.bam -b region.bed > test_intersect.bam
Do you think it's a valid command for my problematic ?