Hello. I have a bed file that contains exons of all mouse ensembl genes. I am trying to get UNIQUE regions which have no overlapping with other ensembl genes. I thought there should be some tools for this, but I haven't been able find one that works. All the tools I found do not remove overlapping regions. Here is a simple example
chr1 10 20 gene1
chr1 15 22 gene2
chr1 20 25 gene3
the result should be
chr1 10 14 gene1
chr1 23 25 gene3
I think this is possible with algorithm using bedtools subtract. But if anyone knows there is a simpler way to do it, I highly appreciate!
Thanks,
RK
chr1 10 20 gene1
chr1 15 22 gene2
chr1 20 25 gene3
the result should be
chr1 10 14 gene1
chr1 23 25 gene3
I think this is possible with algorithm using bedtools subtract. But if anyone knows there is a simpler way to do it, I highly appreciate!
Thanks,
RK
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