Question: Get GC content for a list of intervals in a bed file
0
gravatar for sebastianzeki0
3.3 years ago by
United Kingdom
sebastianzeki0110 wrote:

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?

sequencing • 2.0k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan80k • written 3.3 years ago by sebastianzeki0110

see Calculating Gc Content For All Ccds

ADD REPLYlink written 3.3 years ago by Pierre Lindenbaum108k
0
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

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.

ADD COMMENTlink written 3.3 years ago by Devon Ryan80k
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