Comments on: Ten Favorite Things About Maq http://massgenomics.org/2008/08/ten-favorite-things-about-maq.html Medical genomics in the post-genome era Fri, 27 Apr 2012 18:07:26 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Princess Bride Fan http://massgenomics.org/2008/08/ten-favorite-things-about-maq.html/comment-page-1#comment-136 Princess Bride Fan Wed, 21 Jan 2009 20:26:51 +0000 http://www.massgenomics.org/?p=43#comment-136 The quote is not from "The Princess Bride" but from "Men in Tights" The quote is not from “The Princess Bride” but from “Men in Tights”

]]> By: admin http://massgenomics.org/2008/08/ten-favorite-things-about-maq.html/comment-page-1#comment-118 admin Thu, 28 Aug 2008 16:29:29 +0000 http://www.massgenomics.org/?p=43#comment-118 Thanks to the folks at GT for picking up this post in the Daily Scan: http://www.genome-technology.com/issues/blog/general/149036-1.html Thanks to the folks at GT for picking up this post in the Daily Scan:
http://www.genome-technology.com/issues/blog/general/149036-1.html

]]> By: zee http://massgenomics.org/2008/08/ten-favorite-things-about-maq.html/comment-page-1#comment-117 zee Thu, 28 Aug 2008 02:40:32 +0000 http://www.massgenomics.org/?p=43#comment-117 12. Integration with other aligners if you dont want to use "maq map" to do alignments. In the latest development version of maq there are converters for eland (eland2maq) and novocraft (novo2maq) and you still have the ability to use all those neat downstream tools like assemble, cns2win, cns2snp,mapstat, abpair, mapstat,etc I'll second the point (11), Li Heng is fantastic with helping out on maq-related problems. 12. Integration with other aligners if you dont want to use “maq map” to do alignments. In the latest development version of maq there are converters for eland (eland2maq) and novocraft (novo2maq) and you still have the ability to use all those neat downstream tools like assemble, cns2win, cns2snp,mapstat, abpair, mapstat,etc

I’ll second the point (11), Li Heng is fantastic with helping out on maq-related problems.

]]> By: Ben Berman http://massgenomics.org/2008/08/ten-favorite-things-about-maq.html/comment-page-1#comment-116 Ben Berman Wed, 27 Aug 2008 19:41:53 +0000 http://www.massgenomics.org/?p=43#comment-116 Two more favorites: 10: The Sanger pileup file. This seems like great one stop shopping for track information, including SNPs, quality scores, and position within read if you so desire. 11: Heng. Incredibly responsive to questions and requests One drawback: Maq can spend an inordinate amount of time on low complexity or repetitive sequences. Would be nice to have an option to disregard things with a certain number of seed hits. Two more favorites:

10: The Sanger pileup file. This seems like great one stop shopping for track information, including SNPs, quality scores, and position within read if you so desire.

11: Heng. Incredibly responsive to questions and requests

One drawback:

Maq can spend an inordinate amount of time on low complexity or repetitive sequences. Would be nice to have an option to disregard things with a certain number of seed hits.

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