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

inesdesantiago · 01-30-2009, 11:17 AM

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 · 01-30-2009, 01:39 PM

here is a similar discussion => don't split by chromosome
http://seqanswers.com/forums/showthr...=1020#post1020

inesdesantiago · 01-31-2009, 03:31 AM

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 · 01-31-2009, 11:14 AM

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

bioinfosm · 02-18-2009, 09:44 AM

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

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01-30-2009, 11:17 AM	#1
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	Reference genome for MAQ - split reference genome by chromosome or not? 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

01-30-2009, 01:39 PM	#2
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	here is a similar discussion => don't split by chromosome http://seqanswers.com/forums/showthr...=1020#post1020

01-31-2009, 03:31 AM	#3
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	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...

01-31-2009, 11:14 AM	#4
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	just a quick reply to myself: Yes, that's the right format!

02-18-2009, 09:44 AM	#5
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	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