I have bedg file created from bedtools -
chr1 1 10 num_of_reads chr1 10 20 num_of_reads chr1 20 30 num_of_reads . . .
3th column is information about overlapping reads at this region. I would like to add to 4th column information about GC content in reads from my BAM file. Do you have any idea how to do that? Thank you for any help.
So result should be:
ch start stop num_of_reads cg_content
It is important consider that such measurements will be biased by coverage
Should the cg_content column be expressed as a percentage of bases which are G or C?
better would be just a number - cg content - I now how to calculate separately from bam -
but I need to calculate according BED file.