Comments (3)
0.1 is fairly reasonable. Please note that you end up filtering out any sequence artifacts and stuff like that, which will randomly appear with longer reads.
from methyldackel.
Thanks for the reply! My other question is which count, the count of total reads at this base or count of reads on the non-C strand, is the fraction of non-G reads in the non-C strands compared against?
from methyldackel.
It's the count on the non-C strand, since it's easier to assess whether there's a variant using it.
from methyldackel.
Related Issues (20)
- why cytosine_report output blank file?
- perRead output - print Bismark methylation call string? HOT 3
- Methylation profile for large genome organisms HOT 5
- Chromosomes effected by methylation HOT 4
- 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 HOT 1
- Mixed up reads within bam file
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from methyldackel.