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Old 12-28-2010, 09:10 PM   #1
beliefbio
Junior Member
 
Location: singapore

Join Date: Oct 2009
Posts: 7
Question How to map SOLiD paired end reads by Bfast

1. I found that bfast localalign can't support -1 and -2 options. So I'm confused how it works in
http://seqanswers.com/forums/showthread.php?t=7100
My bfast version is 0.6.4e. Is -1 and -2 work in other versions?

2. Then I tried to merge 2 paired end fastq files into 1 file and run bfast match. But in the bfast postprocess step how to set -r ReadGroup.txt? Could you please show an simple example?

3. The MAPQ of sam files generated by bfast is also Phred scaled, right? If so I can set an cutoff to filter them.
Thanks a lot for you help and time!
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