Using Bwa Sampe Using Illumna Pair End Reads

Question

[Juliofdiaz]

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.

Answer 1

[Zev.Kronenberg]

The *.sai files are generated by first using:

bwa aln

[Zev.Kronenberg]

Yes you first need to aln both reads independently. That will generate the sai files you need to create the SAM file.

[Juliofdiaz]

So first I need to align each read to the ref separately