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.
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.
