Question: WGBS - Methylation state at CpG to peak calls
1
gravatar for Nico Gerstner
3.3 years ago by
Nico Gerstner0 wrote:

Hello everyone,

I have downloaded a WGBS file from ENCODE in bedMethyl format (https://www.encodeproject.org/experiments/ENCSR890UQO/). The content of this file is the methylation state per CpG, e.g.:

track name="SL1615 MspIRRBS" description="GM12878-16_Ximat" visibility=2 itemRgb="On"
chr1    100003153   100003154   ...[omited]      2  0
chr1    1000170     1000171     ...[omited]     22  0

What I want to have is a bed file containing larger regions, somewhat like peaks called from the file above. Is there a tool available that can perform this task?

(My ultimate goal is to use the peak information to state whether an certain region in the genome (e.g. a promoter) can be called "methylated".)

Thank you!

wgbs • 1.4k views
ADD COMMENTlink written 3.3 years ago by Nico Gerstner0
1

some tips here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165320/ I have used methylkit and it appears to work well. http://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html

ADD REPLYlink written 3.3 years ago by mark.ziemann1.3k

Thank you very much for your reply! It seems to me that in the paper and the doc they are calculating differential scores for regions, i.e. they assume I have (at least) two files. Is there a possibility to calculate scores for regions with only one file? (It does not matter if the tool calculates the regions as well, or calculates scores for regions which I provide.)

ADD REPLYlink written 3.3 years ago by Nico Gerstner0

The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp)

ADD REPLYlink written 3.3 years ago by mark.ziemann1.3k

Thank you very much! This was what I was looking for.

ADD REPLYlink written 3.3 years ago by Nico Gerstner0
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