I am trying to map illumina paired reads using BWA and I am having some trouble understanding the workflow. I have two fastq files from the illumina run (read1.fq & read2.fq) and my reference genome in a fasta file(ref.fa). I have first indexed the reference file using:
bwa index ref.fa
and i got the following files
ref.fa.amb ref.fa.ann ref.fa.bwt ref.fa.pac ref.fa.rbwt ref.fa.rpac ref.fa.rsa ref.fa.sa
Now I want to map my illumina reads,and I think the tool I'm looking for is bwa sampe. The help for sampe gives this format.
bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>
I dont quite understand where I'm supposed to get the .sai files from or what those files are. Thanks for any pointers.