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  • Aligning to different regions with BWA

    Hi,
    I was wondering if it is possible in BWA (or perhaps a similar program) to use a reference sequence composed of several different regions. For example if I have several genes which I would like to use. So basically a non-contiguous reference sequence.
    Is there a way to do this without aligning separately to each region? And if so how?

    Thanks for any advice!

  • #2
    Concatenate all of them into a single fasta file and use that as the reference. For example:

    >region_1
    ACGTGT...
    >region_2
    GGCCTG...

    ...etc.

    Comment


    • #3
      Perfect. Many thanks!

      Comment

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