Biostar Beta. Not for public use.
overlap BED files, but account for region name
0
Entering edit mode
20 months ago
igor 7.7k
United States

I recently found ReMap which is a great resource of TF binding sites across different studies. They provide the binding sites in BED format where each region is named based on the TF. Although it's relatively trivial to overlap two BED files (using something like bedtools fisher or bedtools intersect), that assumes that you're just overlapping two sets of regions. Is there a way to generate the results separated by region name? I could split by TF and process each one separately in a giant loop, but that seems inefficient.

ADD COMMENTlink
1
Entering edit mode
13 months ago
Washington University in St. Louis, MO

Your proposal of splitting into separate files by name seems reasonable to me. If that's not satisfying, nothing is stopping you from writing a 20-line perl script that does the intersection in a name-aware manner. Genome set operations aren't hard, it's just more convenient to use existing tools.

ADD COMMENTlink
0
Entering edit mode

Thanks for confirming. I just wanted to make sure I am not reinventing the wheel or missing something.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1