[nilshomer]

Originally Posted by beliefbio

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?

Check out the bfast+bwa version to get that functionality (I assumed you used the bwa functionality instead of bfast match).

For clarity, if you wish to use BWA's "bwa aln" functionality for paired end reads, then you need to align each end independently, merging them together in "bfast localalign" with the "-1/-2" options. Otherwise, the paired end reads should be merged (automatically in solid2fastq) into one fastq file to be processed by "bfast match".

Originally Posted by beliefbio

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?

See the SAM spec on how to create an RG line.

Originally Posted by beliefbio

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!

You can set a cutoff to filter them yes. Better (higher) mapq should correlate with higher stringency.