bwa-mem Roche454

[pingu]

Goodmorning,
(sorry for my bad english), I would use bwa-mem to map sequences against human genome. I have the file fast.q of Roche454 Junior, in this there is not specified if the sequence is in forward or in reverse. In this case, what is the option which allows to use BWA-MEM?
I really hope someone from seqanswer can help me.
Thank you in advance.

[Brian Bushnell]

You never know whether DNA sequences are forward or reverse until after you map them; the mapper will figure that out on a per-read basis. You don't need to do anything special.

The usage is pretty straightforward:

Index:
bwa index ref.fa

Map single-ended reads:
bwa mem ref.fa reads.fq > aln-se.sam

...or, map paired reads:
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam