Hi all,
Hoping someone may know exactly what I did wrong off the bat here since I think we have a lot of BWA gurus here. This is my first time using BWA. Previously I've used Novoalign on the same exome-seq data to great success, aligning the majority of the reads. So I was surprised after running BWA on it that less than 1% of the data mapped and most of it was unmapped.
The data in question are single lanes of HiSeq human exome-seq data.
I indexed the reference genome:
That created (in the same folder):
(I also indexed for colorspace in the same directory since I have SOLiD data I need to align in a few days.)
Then I ran BWA as follows:
There were no errors while it ran except it mapped almost nothing.
Can anyone see a glaring problems in my commands here that would lead to tons of unmapped reads? Any help appreciated!
Hoping someone may know exactly what I did wrong off the bat here since I think we have a lot of BWA gurus here. This is my first time using BWA. Previously I've used Novoalign on the same exome-seq data to great success, aligning the majority of the reads. So I was surprised after running BWA on it that less than 1% of the data mapped and most of it was unmapped.
The data in question are single lanes of HiSeq human exome-seq data.
I indexed the reference genome:
Code:
bwa index -a bwtsw human_g1k_v37.fasta
Code:
human_g1k_v37.fasta.amb human_g1k_v37.fasta.ann human_g1k_v37.fasta.pac human_g1k_v37.fasta.rpac
Then I ran BWA as follows:
Code:
$bwa aln -t 8 $ref $f1 > $out.aln_sa1.sai $bwa aln -t 8 $ref $f2 > $out.aln_sa2.sai $bwa sampe -r "$rg" $ref $out.aln_sa1.sai $out.aln_sa2.sai $f1 $f2 > $out.sam
Can anyone see a glaring problems in my commands here that would lead to tons of unmapped reads? Any help appreciated!
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