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
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bwa reference genome alignment
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
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