Comments (3)
Hello,
We currently are also suffering from a small percentage of reads being completely unconverted. In regards to the --filter_non_conversion
from Bismark, this uses the methylation call strings from a Bismark generated Bam and so doesnt work for non Bismark Bams. So i am just commenting to also express interest in non_converstion filtering for MethylDackel, even if its just something as simple as removing any read with 100% non conversion. I have also commented on another thread on perRead, as if perRead could be given for CHG and CHH metrics, i could use this to filter the reads as well.
Thanks
from methyldackel.
This wouldn't work in the normal extract
, since that essentially operates on a pileup (so looking at the entire length of a read is pretty annoying). I could write a filtering program, but since Felix already wrote one for Bismark I wonder if that'd just duplicate his work needlessly.
BTW, non-CpG methylation does vary in the human genome in accordance with TAD structure and A/B compartments, so I'm hesitant to filter too stringently and end up wiping out something that's actually biologically there (see this article from a collaborator of ours and MethylDackel user as an example).
from methyldackel.
@mattsoup built a simple tool to mark multiple-C reads in a bwameth bam. The tool can set the vendor-fail bit so MethylDackel will skip the marked reads.
It's not battle tested yet.
from methyldackel.
Related Issues (20)
- Understanding --minConversionEfficiency argument HOT 1
- Genome browsing from MethylDackel bedGraphCpG file
- per-fragment methylation HOT 2
- mbias result is different between bismark and bwameth output HOT 1
- CURL_OPENSSL conflict with samtools HOT 3
- Installation failure: "bigWig.h: No such file or directory" HOT 1
- Clarification on definition of "unmethylated C" HOT 1
- Coverage of C sites HOT 1
- mbias HOT 1
- Does indel effect the methylation calling or C context determination HOT 1
- Positions in cytosine_report did not match the regions in providing bed file
- about M-bias HOT 1
- Could not repeat a CpG extraction with the same reference file and its index
- Mixed up reads within bam file
- How to index genome file for MethylDackel? HOT 1
- Confused regarding CTOT, CTOB. Are there suggested values? HOT 3
- Issue running MethylDackel extract in parallel mode using minConversionEfficiency
- Question about minimum coverage
- Different CpG calls when using different regions of inclusion for Methyldackel extract
- Alignment trimming for Soft Clip reads?
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