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Extracting Multiple Mapped reads from Bismark output

Hello everyone

Bismark aligner gives a a report like :

  • Final Alignment report

    Sequences analysed in total: 10000

    Number of alignments with a unique best hit from the different alignments: 6703

    Mapping efficiency: 67%

    Sequences with no alignments under any condition: 2232

    Sequences did not map uniquely: 1065

    Sequences which were discarded because genomic sequence could not be extracted: 0

So,How can I get the reads which are not mapped uniquely with their MAPQ scores and all (like from example 1065 reads)

Thanks Chandan kumar

alignment bs-seq data
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updated by onestop_data onestop_data • written by chaudharyc61 • chaudharyc61

1 answer

I'm not familiar with Bismark, but here it says that the output can be in BAM format. If this assumption is true, you can use a script like this one to convert your BAM2FASTA only targeting the unmapped reads (See Only Unmapped sequences from BAM to FASTA)

I hope it helps.

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written by onestop_data onestop_data

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