make a new bam file

Question

[alireza346]

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?

[WouterDeCoster]

Can you elaborate on why you want to do that? I'm not sure that it's a good idea.

[h.mon]

Even though it is not clear what you want to do, I think bedtools intersect can do what you want.

Answer 1

[btsui]

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).