I am trying to align an assembly to the reference. I used MUMmer in order to obtain a .coords file. Here are my steps in the command line.
1. nucmer --prefix=ref_qry ref.fasta qry.fasta
2. delta-filter -q ref_qry.delta > ref_qry.filter
3. show-coords -rcl ref_qry.delta > ref_qry.coords
How to I obtain 2 FASTA files, one containing the set of sequences that aligns to the reference and one containing the set of non aligned sequences?
I was told I would have to use "parsing" but I'm not sure how to read the headers in the coords file. The labeling isn't explained anywhere in the manual or google.
1. nucmer --prefix=ref_qry ref.fasta qry.fasta
2. delta-filter -q ref_qry.delta > ref_qry.filter
3. show-coords -rcl ref_qry.delta > ref_qry.coords
How to I obtain 2 FASTA files, one containing the set of sequences that aligns to the reference and one containing the set of non aligned sequences?
I was told I would have to use "parsing" but I'm not sure how to read the headers in the coords file. The labeling isn't explained anywhere in the manual or google.