pre-filtering before running alignment: help needed

[angerusso]

Hello All,

I have a WholeExome paired end sample and I reached the step where I am performing the alignment to human genome (hg19.fa) on a 10 node cluster.

I am running the command:
bwa aln hg19.fa sample1_1.fastq > sample1_1.sai
bwa aln hg19.fa sample1_2.fastq > sample1_2.sai

But it's taking forever. I understand this could due to couple of reasons, main reason being that I am not doing any pre-filtering. I saw that packages like GenomeQuest do lot of pre-filtering which can make the alignment faster.

I am total new-bie and i am wondering if I can get help here regarding how and what kind of pre-filtering can I run with this sample before using bwa for alignment. I am kind of in a hurry to get some results so any result will be extremely appreciated.

Thanks,
angel

[colindaven]

Not sure about your cluster configuration, but try using more threads on a single machine of your cluster.

eg
bwa aln -t 8 hg19.fa sample1_1.fastq > sample1_1.sai

[angerusso]

Thanks so much, it works!