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  • shuang
    Senior Member
    • Jul 2011
    • 100

    How to display the sequence of each aligned fragment?

    I used bwasw to align my Illumina reads to a reference genome. Then I use Samtool to pileup to an output.

    In the output, it only shows hetero or homo on the SNP base. But I also want to see thea ctual sequences of aligned fragments, queried reads and aligned genome fragments.

    How do I do it?
  • sdvie
    Member
    • Jul 2010
    • 68

    #2
    To see the sequences of the reads that were aligned, have a look at the .sam file that is output by bwa directly. See here for more information on what you can see in a .sam file:


    Alternatively, or to get a more visual idea of the alignments, you can convert your .sam to .bam, sort and index it using samtools and then use samtools tview. It opens a simple alignment viewer that allows to jump to any position in the reference.

    cheers!

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