Question: Problem with methylKit and Bismark
0
gravatar for ahmad mousavi
2.9 years ago by
ahmad mousavi480
Royan Institute, Tehran, Iran
ahmad mousavi480 wrote:

Hi

I have used Bismark for aligning RRBS reads and now I should run methylKit on bismarks' output, like CpG and bedGraph and .Cov. How can I use these files instead of bam file.

Methylkit manual said it accepts bismark bam file however, I could not handle it. It gives error when I used bismark sorted bam files, and methRead function does not work too.

Does anybody know pipeline for working with bismark output files? I don't mean bam/sam.

epigenetic next-gen • 2.8k views
ADD COMMENTlink modified 2.8 years ago by xuanli10060 • written 2.9 years ago by ahmad mousavi480

Which files did you use the for methRead function?

If it gives you an error, can you post the command?

ADD REPLYlink written 2.9 years ago by igor11k
3
gravatar for jomo018
2.9 years ago by
jomo018610
jomo018610 wrote:

Two step solution: Use coverage2cytosine to convert .cov file to an intermediate file. Then a one-liner awk command or some other script to convert the intermediate file to a methRead input file.

The reason for this two-step process is that .cov lacks strand information.

cov file format:             chr  pos  pos  %meth  #meth  #unmeth
intermediate file format:    chr  pos  strand(+/-)  #meth  #unmeth   na  na 
methRead input file format:  id   chr  pos  strand(F/R)   [#meth+#unmeth]  %meth %unmeth

Where # is (integer) count. The intermediate file contains CG sites not covered by any read and you should discard those in your script.

ADD COMMENTlink written 2.9 years ago by jomo018610
0
gravatar for xuanli1006
2.8 years ago by
xuanli10060
xuanli10060 wrote:

Hi

I have created a file as methylKit input file; it likes the methylKit's test and control samples: chrBase chr base strand coverage freqC freqT 1 chr21.9764539 chr21 9764539 R 12 25.00 75.00 2 chr21.9764513 chr21 9764513 R 12 0.00 100.00 3 chr21.9820622 chr21 9820622 F 13 0.00 100.00 4 chr21.9837545 chr21 9837545 F 11 0.00 100.00 5 chr21.9849022 chr21 9849022 F 124 72.58 27.42

But when I used methRead to read the file, I got errors from this step: Exception: Argument 'file' should be a single value not 7 values. at #17. getVector.Arguments(static, s, length = length, .name = .name) - getVector.Arguments() is in environment 'R.utils'

at #16. getVector(static, s, length = length, .name = .name) - getVector() is in environment 'R.utils'

Error: Argument 'file' should be a single value not 7 values.

Can you help to solve this problem? Thank you very much!

ADD COMMENTlink written 2.8 years ago by xuanli10060

Suggest you show the script lines preceding and including methRead. Please Format the lines with the proper icon.

ADD REPLYlink written 2.8 years ago by jomo018610

I have solved this problem. Thank you for your reply!

ADD REPLYlink written 2.8 years ago by xuanli10060
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