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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"
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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?
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"
The text was updated successfully, but these errors were encountered: