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  • BWA mem on interlaced fastq

    Hi, everybody,

    I am trying to use bwa mem (v. 0.7.12) on some interleaved fastq files, i.e. the reads are paired end, but they are in one file (the ith read is forward; ith+1 is the reverse).

    after indexing the reference genome, I have used the command:

    Code:
    bwa mem -M my_ref.fa -p myfile.interleaved.fastq > ./mapped/my_file.sam
    When I read the log file though, I get this:

    [M:: bwa_idx_load_from_disk] read 0 ALT contigs
    [M:: process] read 117486 sequences (10000027 bp)...
    [M:: process] 117486 single-end sequences; 0 paired-end sequences
    [M:: process] read 118316 sequences (10000081 bp)...

    and so on. Does this mean bwa is not recognizing my reads as paired ends? Have I misunderstood the manual regarding the -p option?
    Looking for advice

    Thanks,
    MAx
    Last edited by mstagliamonte; 04-13-2016, 06:08 AM.

  • #2
    Do the ith read and the ith+1 read have EXACTLY the same name? Please note, that option '-p' is called 'smart pairing'.

    Comment


    • #3
      Thank you, I did not realize it would check for names, thought it would just bluntly take the order of the reads.
      The reads have a bit of an uncommon name, being:

      read1.1 1
      read1.2 1
      read2.1 2
      read2.2 2
      read3.1 3
      read3.2 3

      I'll do a find and replace, see if it works.

      Comment

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