make a new bam file
I have a set of genes including 105 genes. I want to make a new bam file excluding these 105 genes. do you know how I can do that?
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btsui
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alireza346 •
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written
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alireza346 •
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You can use the bed tools complement (http://bedtools.readthedocs.io/en/latest/content/tools/complement.html) to identify the complementary regions, then use bed tools intersect on the bam to extract the complementary regions (http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html).
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Can you elaborate on why you want to do that? I'm not sure that it's a good idea.
Even though it is not clear what you want to do, I think
bedtools intersectcan do what you want.