Using MethylKit with gemBS output files

Question

[N]

Hi,

I was just wondering if anyone is familiar with using gemBS output files for MethylKit such as the ones below

*_3_lane_gembs_cpg.bed.gz

*_3_lane_gembs_cpg.txt.gz

With the following columns

1. Contig
2. Pos0
3. Pos1
4. Ref
5. Call
6. Flags
7. Meth
8. non_conv
9. conv
10. support_call
11. total

I tried running methylKit but it has trouble with with columns 5 and 6. My question is how would I format it in a way that MethylKit would recognize and process for differential methylated region (DMR) analysis. What columns are not needed and can be removed safely or have to be merged in order to run. I tried searching it online and the other methylation call files have very different columns. Could anyone with experience in DMR analysis provide some advice for this type of analysis with this type of file.

Thank You!

Answer 1

[Tian]

I have recently encountered this issue, tried to solve it as my post here:

https://yuantian1991.github.io/notes/Import-GemBS-output-into-methylKit