Get GC content for a list of intervals in a bed file
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?
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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.
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Devon Ryan
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See Calculating Gc Content For All Ccds