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Hello,
I'm using NUcmer and mgaps from MUMmer to find indels between a reference and a draft genome. The mgaps output is neat and almost exactly what I want, but not ordered according to where the query sequences map in the reference. Is it possible to reorder the query sequences (the contigs) according to the reference?
The reason I care is that I want to find the "density" of variation in different parts of the genome. If I can get the contigs reordered then it's just a matter of counting the #'s under each contig (signifying different clusters) and applying some kind of normalization by contig length. Or something like that.
I'm using NUcmer and mgaps from MUMmer to find indels between a reference and a draft genome. The mgaps output is neat and almost exactly what I want, but not ordered according to where the query sequences map in the reference. Is it possible to reorder the query sequences (the contigs) according to the reference?
The reason I care is that I want to find the "density" of variation in different parts of the genome. If I can get the contigs reordered then it's just a matter of counting the #'s under each contig (signifying different clusters) and applying some kind of normalization by contig length. Or something like that.