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  • discordant paired-end reads

    Hi Everyone,

    May be a simple question, but I am having trouble finding it. I did extensive search for weeks and finally, seeking your help.

    I have solexa paired-end sequences. I am trying to find the discordant paired-end reads. I used MAQ and output the unmapped reads. Are they the discordant pairs or should I find the discordant pairs in mapped reads of MAQ?

    Is it possible to use BOWTIE or BWA to find discordant pairs? If so, what option should I use?

    Any help will be appreciated.

    Thanks,

    Sathish

  • #2
    This is just a suggestion of the top of my head so it might not be correct.

    Maybe you could manually reverse-complement one side of the pairs with a small script and then align these modified pairs with a standard aligner?
    SpliceMap: De novo detection of splice junctions from RNA-seq
    Download SpliceMap Comment here

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    • #3
      With 'bwa aln' and 'bwa sampe' its very easy to find those pairs. Using a bit of perl even different categories of discordant pairs may be easily identified like:
      mates on different chromosome
      mates on the same strand
      mates with a weird distance
      etc

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