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  • Reverse complementary reads in Mummmer

    The repeat-match program in mummer, claims to return reverse complementary repeats, and mark them with 'r'. However, I found that the repeats returned are complementary repeats, not reverse complementary.

    For example if position 10-14 in my sequence are AAGG and position 20-24 are TTCC, these are not reverse complementary repeats but mummer repeats them. Am I doing something wrong here?

    Further, do complementary repeats even matter in genome assembly. Reverse complementary repeats matter, but I do not think complementary repeats should matter as the reads we get from the forward and reverse strands are in opposite directions.

    Edit: sorry the title should have been Reverse complementary repeats in Mummer, rather than Reverse complementary reads in Mummer.
    Last edited by gkamath; 08-05-2014, 11:19 AM. Reason: typo in title

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