[mira_talk] Re: convert_project error
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Jul 2010 12:13:55 +0200
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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