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Old 11-10-2009, 12:44 AM   #1
fatseq
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Default get maq map output - maqview application

Hi people, Iīm new here and currently working on my first sequencing data which is Illumina GA2 data. I used maq for the alignments, but now I donīt know how to get the alignment data into a nicer format than the ".map"-files. Is there any tool someone can recommend, like maqview, to visualize the alignments? and how do I get a readable format? I used the "maq mapview" option but this only displays the results to the screen, how can I put the data into a new file? Should I use the "mapmerge"-command to do this?
I would be happy to get an opinion and/or advice on this...although my problems are probably trivial :-) to you. Many thanks!
fatseq
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Old 11-10-2009, 01:31 AM   #2
jkbonfield
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Li Heng maintains a list of alignment viewers at http://lh3lh3.users.sourceforge.net/NGSalnview.shtml

You may also want to consider changing it from maq to sam/bam format for some tools, depending on precisely what you want to do downstream.

James
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