bwa reference genome alignment

[nxtgenkid10]

I like to know how to run bwa to align my pe reads to the reference genome

first i tried to create the reference of the bac genome bwa index -a is /Reference/ref.fa

I tried the following command to align
bwa sampe /DATA/Read1.fastq /DATA/Read2.fastq

But i couldn t find an option to put my reference sequence for alignment

and should i use bwa aln also if so y and how?

Thanks

[dpryan]

Have you read the BWA manual page?

[vishnuamaram]

Hey nxtgenkid10

if your data is paired end, this is the way you should go.

1) bwa index ref.fa = index your ref. genome.

2) bwa aln ref.fa short_read.fq > aln_sa.sai = get sai files for both reads, say read1 & read2.

then do

3) bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam