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MM/ML tag and hard/soft clipping alignments #1066

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PanZiwei opened this issue Mar 3, 2023 · 1 comment
Closed

MM/ML tag and hard/soft clipping alignments #1066

PanZiwei opened this issue Mar 3, 2023 · 1 comment

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@PanZiwei
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PanZiwei commented Mar 3, 2023 •
edited

Hi,
I am wondering whether you have a following up solution for the samtools/hts-specs#646. How does Nanopolish do alignment currently? It's soft-clipping or hard-clipping?
Thank you!
@jts
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jts commented Mar 3, 2023

Nanopolish relies on the alignment in the .bam file provided by the user, which is usually from minimap2. I'm going to close this issue so that the discussion about hard clipping is in one place (in the hts-specs issue)

@jts jts closed this as completed Mar 3, 2023
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@jts @PanZiwei