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Old 01-26-2009, 09:43 AM   #1
jyli
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Location: North Carolina

Join Date: Nov 2008
Posts: 21
Default MAQ command

Hi all-

I have a question about MAQ software. At the website, http://maq.sourceforge.net/maq-man.shtml, one of the key commands listed was maq MATCH -param, etc. However in their manual documentation: http://maq.sourceforge.net/maq-manpage.shtml, the command is "map MAP -param etc". Does anyone know whether these two are same?

When I tested on a sample data, I found some alignment results were different because it reported on different strand. Apparently, both matches/alignments were valid. My question is how/whether I can retain both results, as in the .map file, it showed either or but not both?

Any attention is appreciated.

Thanks.
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