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Coverage of reads when using umi mode #71

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korakusa opened this issue Apr 20, 2022 · 1 comment
Open

Coverage of reads when using umi mode #71

korakusa opened this issue Apr 20, 2022 · 1 comment

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@korakusa
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Dear developers:
Thank you for the wonderful tool.

Is there any way to know the coverage of reads when using --umi mode?
In umi mode, only read with UB tag is considered, so I think that the coverage is different from that in non-umi mode.
Is my understanding correct?

If so, how do I know the coverage of reads when using umi mode?
One way I came up with is to filter the input bam file to only the reads that have the UB tags in advance, but does this give me the result I want?

Thanks a lot in ahead.

@korakusa
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Dear developers,

In order to reduce calls due to sequence error, I would like to use umi mode and further filter by the number of mutant reads. Please tell me if there is a way to know the mutant read count when running umi mode.

Thank you.

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