how to extract methylation level of certain genomic regions?
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7 months ago
hksk2 ▴ 10

I have mapped my WGBS data and calculated methylation levels and I have a list of genomic regions that want to extract methylation levels from my methylation data.

The list of genomic regions look like this

Chr       start      end
1        103564    105566
2        701250    702223


and the methylation levels of my sample data obtained from bsmap look like this:

chr pos strand  context ratio   eff_CT_count    C_count CT_count    rev_G_count rev_GA_count    CI_lower    CI_upper
1   10004   +   AACCC   1.000   1.00    1   1   0   0   0.207   1.000
1   10005   +   ACCCT   1.000   1.00    1   1   0   0   0.207   1.000
1   10006   +   CCCTA   1.000   1.00    1   1   0   0   0.207   1.000


Is there any program or script that can do this? I know I can extract one by one but there are 790 regions on the list and I have 24 samples..

methylation bsmap CpG wgbs • 258 views
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check out bedtools intersect function