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Position of all cytosines in retention pattern #37

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shahmj opened this issue Jan 24, 2020 · 0 comments
Open

Position of all cytosines in retention pattern #37

shahmj opened this issue Jan 24, 2020 · 0 comments

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@shahmj
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shahmj commented Jan 24, 2020

Hi,

In the single-end epiread format one of the fields in the output is "5) position of the cytosine in the first CpG (0-based)". Is it somehow possible to get length of the alignment or position of remaining cytosines for all CpGs covered by the read? I would like to consider CpGs within a certain distance from the first one.

Thanks,
Minita
zwdzwd pushed a commit that referenced this issue Aug 13, 2023
@jamorrison
Fix Issue #37
6664918 
This brings the BISCUIT MD tag into alignment with the MD hts-spec.
Note, the NM tag only shows the number of non-cytosine-conversion
mismatches. To recreate the NM tag produced by samtools calmd, add the
NM tag and ZC tag together.
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@shahmj