Comments (6)
dpryan79
commented on June 24, 2024
What was the exact command you used that produced that?
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yij047
commented on June 24, 2024
Just called MethylDackel extract with no arguments (just the fasta and bam). Using the perRead branch.
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yij047
commented on June 24, 2024
MethylDackel extract Homo_sapiens.fasta mega.bam
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dpryan79
commented on June 24, 2024
I'm stumped, I'm not really sure how that's happening. Is it possible for you to subset the BAM file to just include that region and see if that reproduces the issue? Then you can post that somewhere and I can try to track this down using that.
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yij047
commented on June 24, 2024
Yeah thank you still. I realize there're dots in the 5th column and 6th column as well. Not sure why.
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dpryan79
commented on June 24, 2024
If you're able to make an example of this available please reopen so I can have a look.
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Related Issues (20)
- Stand output HOT 1
- 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
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