Generating 5mCG or 5hmCG values per gene from BS/OXBS data
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hasche • 0
Last seen 11 weeks ago
United States

Hi, I use the methread function to read the coverage files from Bismark. BS_21=methRead("2368_bismark_bt2_pe.deduplicated.bismark.cov.gz","2368_BS",assembly="mm10", header=F,skip=0,sep="\t",context="CpG", pipeline="bismarkCoverage", mincov = 5) However, the resulting methylkit object seems to lose the methylation percentage values generated by Bismark.



While I have found out a quick way of incorporating the meth %s for each methylation call from BS-seq experiments; the same is tricky when it comes to 5hmC data that I derive using the adjustmethylC function (because then I have two meth %s; one from BS and other from OXBS).

Would a plain subtraction of percent.meth per CpG (derived from Bismark) (BS minus OXBS) be the ideal way to go?

N.B. As expected, I have way more methylation calls from BS than the OXBS experiment.

I think that this whole situation stems from the fact that after running methread; the percentage methylation values of the coverage output from Bismark are lost.

My end goal is to generate 5mC and 5hmc signals per gene.

Please advise.

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