[mira_talk] RE Re: Inconsistent unpadded reads length in ACE file

From: Jorge.DUARTE@xxxxxxxxxxxx
To: mira_talk@xxxxxxxxxxxxx
Date: Tue, 1 Jun 2010 10:04:43 +0200
Hi,

i faced the same problem and solved it by using some of the caftools.

Before to run gigabuild, you should run these commands :

caf_depad < mira_out.caf > mira_out_unpadded.caf

and

caf2phrap -caf mira_out_unpadded.caf -fasta mira_out_reads.fasta -clip

this command will generate 3 files :
mira_out_reads.fasta
mira_out_reads.fasta.qual
mira_out_reads.fasta.ace

(I'm not sure about the -clip option, but i had some problems when not 
using it)

Then you just have to run gigabuild like this :

gigaBuild --ace mira_out.ace --gig mira_out.gig --fd mira_out_reads.fasta 
--fq mira_out_reads.fasta.qual

Now you are ready to run gigaBayes, it should work properly with this gig 
file.

Although, in some rare cases, there is still a one base difference in snp 
positions reported by gigabayes
and the ones reported by mira, but i still did not find a workarround.

I do agree with Bastien, that it would be much more efficient to start 
from another file format than the ace format which do not include read 
qualities,
but i do understand the authors of GigaBayes since the ace format is 
widely used.

I wish everyone would agree on a common format some day, i'm tired to look 
for the right converter,
but i'm not very optimistic about that ;-)

Thankfully people like the authors of caftools and Bastien released and 
try to maintain some of these converters...

jorge.

--- 
Jorge Duarte
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Z.I. Du Brézet
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FRANCE
Tel : +33 (0)4 73 39 60 73
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E-mail : jorge.duarte@xxxxxxxxxxxx

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mira_talk-bounce@xxxxxxxxxxxxx a écrit sur 31/05/2010 19:50:12 :

> On Montag 31 Mai 2010 Davide Scaglione wrote:
> > Hi Bastien,
> > thanks again for your support about heterozygous SNPs assembly.
> > Now I'm facing another problem, the following.
> > I'm using gigaBayes to mine SNPs form the ACE file.
> > While using a small dataset of Sanger sequence (the same you used to 
look
> >  at my SNPs problem) everything run fine. Now, using 450000 454 
sequences,
> >  the first module of gigaBayes (I don't if you ever played with it) 
abort,
> >  returning me an error because there is inconsistency between the read
> >  length in the input file and the unpadded read length in the ACE file 
(so
> >  far the difference I found is one base).
> 
> You might want to read this post:
> 
> //www.freelists.org/post/mira_talk/Some-nt-missing-in-the-assembly-
> files,1
> 
> > Thus, I'm stack; I have no idea how to play around this and fix this
> >  inconsistency (I didn't see any parameters which might be related). 
Am I
> >  doing something wrong?
> > [...]
> > 454_SETTINGS
> > -ED:ace=yes
> 
> Don't turn on the automatic contig editor is your only chance.
> 
> Of course, you might as well ask the authors of gigabayes to write an 
import 
> filter for assembly format which do not have the flaws of ACE. Did I 
already 
> mention Ace is a horrible format? No?
> 
> Bastien
> 
> "Ceterum censeo, ACE esse delendam."
> 
> 
> Oh, did I already mention that ACE is a horrible format?
> 
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[mira_talk] RE Re: Inconsistent unpadded reads length in ACE file

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