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  • Low Pairing of R1 and R2

    Hi Guys,

    It happened with only 1 sample, For others it was all good.

    Pairing was low 10.99%. Normally for other samples, I am getting around 80%. What could go wrong with it.

    The pipeline was BWA-MEM with default parameters + samtools. rna 2*150bp

    Below is the output from flagstat


    SAM tools FlagStat
    AB612
    2394946 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 secondary
    37488 + 0 supplementary
    0 + 0 duplicates
    2366833 + 0 mapped (98.83% : N/A)
    2357458 + 0 paired in sequencing
    1178729 + 0 read1
    1178729 + 0 read2
    259168 + 0 properly paired (10.99% : N/A)
    2320108 + 0 with itself and mate mapped
    9237 + 0 singletons (0.39% : N/A)
    58364 + 0 with mate mapped to a different chr
    5947 + 0 with mate mapped to a different chr (mapQ>=5)

  • #2
    Have you checked to make sure that your input sequence files are in sync as far as R1/R2 go. You can use `repair.sh` from BBMap suite to bring them in sync if they are not (e.g. if mates are missing from one or both files).

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