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Pierre Lindenbaum
Extract reads from specific target in .bam file
Hi all,
I am looking to extract reads that are mapped to a specific target.
Let's say I have a file target.txt like this:
head target.txt
scaffold1
scaffold2
scaffold3
And an another file which is a bam file.
Is there a tool that extract reads (or filter) that have mapped only on my target ? ( I have one bam with paired reads and one bam with single reads).
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