Reference genome for MAQ - split reference genome by chromosome or not?

[inesdesantiago]

Hello!
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 output.map 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?
THanks!!
ines

[bioinfosm]

here is a similar discussion => don't split by chromosome

http://seqanswers.com/forums/showthread.php?p=1020#post1020

[inesdesantiago]

Good to know!

I can't find the complete genome in the UCSC database.
Should I do it myself? merge my chromosome.fa files into one-big file looking like this:

>chr1
AACTGTGCACTGTGACAC...
GTACGCACGTGCGTGCAC...
>chr2
ACATTGCCAACACTGTCA...
ACACGTGCGTGCACACGT...
>chr xyz

I don't know if this is the right format...

[inesdesantiago]

just a quick reply to myself:
Yes, that's the right format!

[bioinfosm]

Yes, sometimes eland gives issues with fasta headers, it creates extra columns in the export or eland_extended output. So I also prefer to keep the fasta reference sequence headers small