1. I found that bfast localalign can't support -1 and -2 options. So I'm confused how it works in
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!
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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