[mira_talk] Re: contigs built only by one sequence
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 21 Dec 2009 13:12:32 +0100
On Donnerstag 17 Dezember 2009 Laurent Manchon wrote:
> --Hi,
>
> i have made assembly on 454 reads (~600 000 reads) using mira 2.9.43 and
> with this command line:
>
> bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454
> -notraceinfo -GENERAL:kcim=yes,not=3 -SK:rt=4
> -CO:fnicpst=yes,rodirs=10,asir=yes
> -CL:cpat=no,pec=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc
> =yes,mrcr=0,smrc=0
> -AL:bip=5,bmin=10,mrs=90:egp=yes:egpl=reject_codongaps:megpp=100,mo=60
> -AS:mrl=30,bdq=30 -SK:mnr=yes,rt=8,mmhr=6
>
> and i obtain 53867 contigs but some contigs (~18163) are only built
> using one sequence, why ?
> So, i don't understand...
> I thought that contigs established(constituted) by a single sequence was
> singulets and had to appear in debrislists, don't you ?
The default for this command line is to still save tagged singlets:
Save tagged singlets in project (stsip) : [san] yes
[454] yes
so I suppose those reads were tagged in earlier passes. If not, please confirm
the current version has the same behaviour and tell, this would be a bug.
Regards,
Bastien
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