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idxstats count of mapped reads #14

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josephhughes opened this issue Mar 2, 2022 · 1 comment
Open

idxstats count of mapped reads #14

josephhughes opened this issue Mar 2, 2022 · 1 comment

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@josephhughes
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Add a count of mapped reads at the moment weeSAM uses idxstats that "may count reads multiple times if they are mapped more than once or in multiple fragments"

@jonbra
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jonbra commented Mar 6, 2024

I also wonder about this. Is it so that the number of mapped reads is based on the output of samtools idxstats? Because I think this outputs mapped "fragments", which I think corresponds to "read pairs" if that was the input? So this number would roughly correspond to mapped read pairs and not mapped reads?

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