Get GC content for a list of intervals in a bed file

Question

[sebastianzeki0]

I have a list of intervals in bed file format eg

chr      chromStart       chromEnd
chr1     13223            13999
chr2     1111             22222

etc.

I would like to ascertain the GC density within the whole interval (or just before, just after etc- basically wherever I specify). Is there a way to do this easily from a bed file ( I don't have raw sequences) for all the intervals at the same time?

[Pierre Lindenbaum]

See Calculating Gc Content For All Ccds

Answer 1

[Devon Ryan]

You can do this easily enough in R. Here's a script that demonstrates how to do that for genes in a GTF file. A BED file would be even simpler.