Intrastrand CpG Methylation Data

Question

[NGS-Newbie]

Hi All

Does anybody know of a program or a way to extract CpG methylation data within the same strand (for a set number of reads) for a targeted bisulfite sequencing 150 PE reads?

Thank you all!

[NGS-Newbie]

Thanks so much, Devon Ryan!

What I am trying to achieve is the following -

Background: 150 PE, targeted bisulfite sequencing, Illumina platform. I have both separate files of read pairs (R1 & R2) and a combined file of merged reads as well.

Assuming there are five CpG sites in the 300 bp (merged read) region of interest - CpG1, CpG2, CpG3, CpG4, and CpG5; would it be possible to get a file with an output as follows -

        CpG1        CpG2        CpG3        CpG4        CpG5

Sequence Read 1 Met Met Met Met Met Sequence Read 2 unM Met Met Met Met Sequence Read 3 Met unM Met Met Met Sequence Read 4 Met Met unM Met Met Sequence Read 5 Met Met unM unM Met

Met = Methylated; unM = Unmethylated. It could be a Yes/No or 0/1 output. I would like to be able to do that for say 100/500/1000 reads.

Any suggestions?

Thank you all so much!

[Devon Ryan]

MethylDackel won't give you per-read metrics, since that's rarely useful.

Answer 1

[Devon Ryan]

You can use MethylDackel with either the --OT or --OB options to clip off all of the bases from a given strand.