Question: Using Bwa Sampe Using Illumna Pair End Reads
0
gravatar for Juliofdiaz
7.0 years ago by
Juliofdiaz130
Toronto, Ontario, Canada
Juliofdiaz130 wrote:

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.

illumina paired bwa • 5.1k views
ADD COMMENTlink written 7.0 years ago by Juliofdiaz130
4
gravatar for Zev.Kronenberg
7.0 years ago by
United States
Zev.Kronenberg11k wrote:

The *.sai files are generated by first using:

bwa aln
ADD COMMENTlink written 7.0 years ago by Zev.Kronenberg11k
1

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

ADD REPLYlink written 7.0 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 7.0 years ago by Juliofdiaz130
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