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Old 09-10-2013, 10:48 AM   #1
prs321
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Join Date: Jun 2013
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Default Alignment of assembly to reference (nuclear genome) [MUMmer]

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.
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