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Alignment trimming for Soft Clip reads? #158

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iiiir opened this issue May 12, 2024 · 0 comments
Open

Alignment trimming for Soft Clip reads? #158

iiiir opened this issue May 12, 2024 · 0 comments

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@iiiir
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iiiir commented May 12, 2024

Hi,
I wonder if methyldackel trim reads before or after softclip reads?
e.g. if i desired to trim 5bp each side for every read with --nOT 5,5,5,5
for a read with CIGAR string 5S1146M or 146M5S, is it 5 bp trimmed (only the soft clipped bases) or actually 10 base will be trimmed (5soft clip + 5 trimmed)?
Thanks much!!

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