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  • BWA: Should Sai/Sam sequences processed match

    Hi,

    After running BWA I get an output like this:

    [bwa_sai2sam_pe_core] print alignments... 0.66 sec
    [bwa_sai2sam_pe_core] 197538574 sequences have been processed.
    [main] Version: 0.6.1-r104

    Should the no. of sequences processed match for the sai and sam files?

    For both sai files I have the no. of sequences processed at 147913358
    For the sam file it is 197538574

    I have re-run this but get the same result. For other sai to sam conversions I have run this number seems to match.

    Thanks,

    Jom

  • #2
    Given your data is PE, there is no reason the number shouldn't match really. Could be pairing messed up. How many reads do you have in each fastq then?

    Best,

    Dong

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