Comments (4)
I suppose so. Keep in mind, though, that this will end up being per-base (overlapping a CpG) per-read, so the numbers will probably look disturbingly high.
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Great, thanks.
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Similar question: would it be possible to have some kind of alignment report akin to Bismark's, where sequence pairs that are not used are reported? I.e. some alignments are not used due to low MAPQ or low Phred and some supplementary alignments are discarded; it would be nice to know how many of the sequenced read pairs are used for the methylation calls.
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@nchernia I'll see what I can do. The functions that filter reads by MAPQ/flag are buried pretty deep in the code. The phred filtering stuff happens for each base, so I'll try to come up with a reasonably meaningful aggregate value for that.
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Related Issues (20)
- 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 HOT 1
- 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?
- Can MethylDackel extract per-base methylation metrics for TAPS?
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