This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Using Bwa Sampe Using Illumna Pair End Reads

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.

bwa illumina paired
• 7,641 views • link
updated by Zev.Kronenberg Zev.Kronenberg • written by Juliofdiaz Juliofdiaz

1 answer

The *.sai files are generated by first using:

bwa aln
• 0 views • link
written by Zev.Kronenberg Zev.Kronenberg

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

• 0 views • link
written by Juliofdiaz Juliofdiaz

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

• 0 views • link
written by Zev.Kronenberg Zev.Kronenberg

Log in to answer this question.

More posts like this