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From: Afif E. <ael...@sd...> - 2015-11-02 20:17:41
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Hello, I am trying to get a very basic comparison between a de novo assembled microbial genome and a reference sequence. I used nucmer at first, but there was a tandem duplication that was causing overlapping alignments and I just wanted to know precisely what was different. It appears that the plain mummer program would be appropriate for finding this out, so I called mummer as follows: mummer -mum <reference> <query> By using the -mum flag, I thought that I'm not supposed to be seeing any overlap in the matches in both the query and reference, but I found an instance of this in those positions where I was previously getting overlaps in my nucmer alignments: 3569553 3570622 132349 3701734 3702919 39749 If I understood the format of the output correctly, the first match here overlaps the second in the reference (3569553+132349 = 3701902 > 3701734) and the query. By manual inspection of blast results of these positions, I know that there is a tandem repeat in this region where the query has five copies and the reference has three copies and the overlap in the matches here matches all three copies in the reference twice and also matches one of the copies in the query twice. This doesn't look to me like intended behavior of the program, especially since I'm not using -maxmatch. Am I doing something wrong or misunderstanding anything here? I'm using MUMmer 3.23 as packaged in Debian 8. I can provide my query genome privately if necessary. Many thanks and regards Afif -- Afif Elghraoui Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence San Diego State University Alvarado Medical Center 6367 Alvarado Court, Suite 206 San Diego, CA 92120 p. 858-222-0454 http://tuberculosis.sdsu.edu |