Hi everybody:
supposed that:
1. reference file: hg19.fa
2. solexe data: 1.fq.gz
and i do bwa index and aln like the follow:
bwa index -a bwtsw hg19.fa
bwa aln -t 2 -n 2 -o 1 -e 5 -q 20 hg19.fa 1.fq.gz >1.sai 2>1.sai.sterr
am i right?
and what's the difference between the formal hg19.fa and the hg19.fa indexed.thank you very much. yours help is greatly appreciated.Best wieshes.
supposed that:
1. reference file: hg19.fa
2. solexe data: 1.fq.gz
and i do bwa index and aln like the follow:
bwa index -a bwtsw hg19.fa
bwa aln -t 2 -n 2 -o 1 -e 5 -q 20 hg19.fa 1.fq.gz >1.sai 2>1.sai.sterr
am i right?
and what's the difference between the formal hg19.fa and the hg19.fa indexed.thank you very much. yours help is greatly appreciated.Best wieshes.