Rsamtools : Extracting Unmapped Reads from BAM file
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polemiraza ▴ 70
@polemiraza-11428
Last seen 2.7 years ago
Poland

Does anyone have any experience extracting unmapped reads from BAM file and saving them in a new BAM file using Rsamtools (or any other R/Bioconductor package) ?

I am analysing paired-end RNAseq data processed by Rsubread package.

If you could provide some generic code to address this problem it would be greatly appreciated.

Unmapped RNAseq Rsamtools • 1.9k views
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What have you tried?

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@martin-morgan-1513
Last seen 1 day ago
United States

Use filterBam() to create a new file from a subset of the original file, using the ScanBamParam() argument to select just unmapped reads. The help page ?filterBam includes this example

     param <- ScanBamParam(
        flag=scanBamFlag(isUnmappedQuery=FALSE),
        what="seq")
     dest <- filterBam(fl, tempfile(), param=param)
     countBam(dest)  ## 3271 records

(the flags can be complicated, so verify that this selects the reads you're interested in).

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Thank you Martin! The code you provided worked for me!

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