Entering edit mode
6.8 years ago
NGS-Newbie
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10
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!
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 -
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!
MethylDackel won't give you per-read metrics, since that's rarely useful.