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
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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