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  • BWA MEM question

    Dear all,

    I just have a question about bwa mem alignment. I ran the following simple command:

    bwa mem <fa> <fastq> -t 5

    Before the alignment I checked the number of reads with fastqc and then after alignment I counted the IDs present in the sam file with grep '<common ID> | wc -l and I got different results.
    What causes the difference? Is the multi-mapper reads present in the sam file?

    Total reads: 24 961 320
    Aligned reads: 24 961 535

    Thank you for the answere,
    Regards,
    Liy

  • #2
    Run
    Code:
    samtools view -S -f 0x100 <file.sam>
    to get the multimappers.
    Last edited by sarvidsson; 02-24-2015, 06:54 AM. Reason: too quick

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