[mira_talk] Re: convert_project error
- From: "Reiff, Caroline" <caroline.reiff@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 Jul 2010 13:24:39 +0100
Thanks for the reply- I have just noticed that convert_project works perfectly
with the maf file as input- so that solves my problem. I take it it does not
matter whether you use the caf or maf file as input to make the result tables?
So maybe it is a bug in the convert_project script???
Caroline
Caroline Reiff
Next Generation Sequencing Bioinformatician
Aberdeen University
School of Medicine & Dentistry,
Division of Applied Medicine
Polwarth Building Room 2:028
Aberdeen
AB252ZD
Telephone: 01224 559178
e-mail: caroline.reiff@xxxxxxxxxx
http://www.abdn.ac.uk/ims/facilities/bioinformatics/
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf
Of Lionel Guy [guy.lionel@xxxxxxxxx]
Sent: Thursday, July 22, 2010 11:13 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: convert_project error
Hi Caroline,
It's not your input files nor a bug. MIRA indeed adds a "n" in front
of all solexa reads. If I correctly recall, this was in order to store
a read tag. FYI, it also edits solexa reads without tracking the
changes
(//www.freelists.org/post/mira_talk/MIRA-silently-edits-lowqual-solexa-reads,1
)
I don't know about the convert_project errors.
HTH,
Lionel
On 22 Jul 2010, at 11:31 , Reiff, Caroline wrote:
> Hi,
> I have done an assembly with MIRA and I tried both accurate and
> normal mapping assembly, both resulted in good assembly:
> mira --fastq --project=data --job=mapping,genome,accurate,solexa -
> SB:lsd=yes:bsn=Myco_t_KZN1435:bft=gbf
> mira --fastq --project=data --job=mapping,genome,solexa -
> SB:lsd=yes:bsn=Myco_t_KZN1435:bft=gbf
>
> I then wanted to use the convert_project function. For some reason
> convert_project throws and error stating that the sequence and
> quality are not the same length (I already posted this problem). I
> have now looked at the caf file and sequence and quality are
> actually the same length but I noticed in the caf file that MIRA
> inserted an n at the start of each sequence and a 0 at the start of
> each sequence quality and wonder if this is normal or if this is a
> bug in MIRA or more likely something to do with my input sequences?
>
> Thanks Caroline
>
>
> Caroline Reiff
> Next Generation Sequencing Bioinformatician
> Aberdeen University
> School of Medicine & Dentistry,
> Division of Applied Medicine
> Polwarth Building Room 2:028
> Aberdeen
> AB252ZD
>
> Telephone: 01224 559178
> e-mail: caroline.reiff@xxxxxxxxxx
> http://www.abdn.ac.uk/ims/facilities/bioinformatics/
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
>
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