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Old 01-30-2009, 11:17 AM   #1

Join Date: Jan 2009
Posts: 44
Cool Reference genome for MAQ - split reference genome by chromosome or not?

I am a beginner!
I am trying MAQ..
My question is about the reference genome! I downloaded the mm9 genome from UCSC, and it comes as separated chr*.fa files (one fasta per chromosome)

However, the MAQ command to do the alignments points to a single file as the reference genome:

maq match genome.bfa myreads.bfq

I converted all my chr.fasta files to bfa files using maq "fasta2bfa".
Now, I don't know if i am supposed to run the MAQ for each single chromosome individually or if I should have the complete genome in one-single-bfa-file.

Any of these is a challenge.
If we the alignment is to run chromosome by chromosome then there should be a way to merge the output files (I think...!?).
One the other hand, if the genome is supposed to be in just one-file, how do I do that?

Any thoughts?
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