I am trying to use Bfast to map Solid data to a reference genome. I ran through the work flow as suggested in the manual book. Finally I got output files xxx.sam, but I could not make sense of those files.
How can I make use of SAM files? What I wanted to get out of the mapping results are basically the correspondance between reads and matched reference sequences, for example,
Read1 <----> Ref3, matched from starting pos of xxx
Read2 <----> Ref8, matched from starting pos of xxx
Are there some tools available for doing this?
Thanks a lot!
How can I make use of SAM files? What I wanted to get out of the mapping results are basically the correspondance between reads and matched reference sequences, for example,
Read1 <----> Ref3, matched from starting pos of xxx
Read2 <----> Ref8, matched from starting pos of xxx
Are there some tools available for doing this?
Thanks a lot!
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