Counting Distinct Mapped Reads in BAM File of Paired-end Sequencing
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 25 days ago
Australia

Is it possible to determine the distinct number of reads in a BAM file using countBam, if some of the fragments have both read pairs mapped and some have just one of the two reads mapped ? I want each situation to be only counted once towards the grand total.

rsamtools paired-end reads countbam • 1.0k views
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@martin-morgan-1513
Last seen 4 days ago
United States

Perhaps use

param = ScanBamParam(
    flag = scanBamFlag(isFirstMateRead=TRUE))
countBam(..., param=param)

to count only the first (i.e., the only read of a single-end read, or the first of a paired end read) read? Perhaps with additional flags?

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It wouldn't be possible to easily count multi-mapping reads only once with this approach. I suppose the most general solution would be to do length(unique(scanBam(bamFile, param = ScanBamParam(what = "qname"))[[1]][[1]])).

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