[mira_talk] Re: Too high coverage contig
- From: Adnan Niazi <niazi84@xxxxxxxxxxx>
- To: mira talk <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 24 May 2011 18:10:34 +0000
Hi,
Thanks all. I will try your suggestions. But one more question, the problem is
that GAP4 is not working for me right from the beginning of my work
(installation problem). Is it possible by some other means to dump all the
reads for that particular contig into a fastq or even in fasta format and then
assemble those reads with parameters suggested below? If not then i think i
will have to reassemble all the reads again for sure. Thanks again for your
cooperation.
regards,
adnan
> Hi,
>
> as a start, I would try to assemble your reads with the
> --highlyrepetitive flag, so that the micro-heterogeneity in reads is
> better taken into account.
>
> This has worked pretty well for me. There are also some options that you
> can tweak to get a better result (such as -AS:urdcm=1.1:ardml=100), but
> I would first try the --highlyrepetitive flag and then maybe tweak some
> specific parameters.
> On 24/05/11 17:40, Fernando Martínez-Alberola wrote:
> > Hi all!
> >
> > I think you can open your assemble in gap4 and breack you contig in
> > different contigs if there are reads with differences (SNPs?) between
> > them and make find internal joints against thouse new contigs for fill
> > your gaps.
> >
> > I do not know if this is correct, may be some guru can answer you better
> > than me!
> >
> > Regards, F.
> > El lun, 23-05-2011 a las 21:20 +0000, Adnan Niazi escribió:
> >> Hi all,
> >>
> >> I have found a contig of 5kb in the denovo assembly which has too high
> >> coverage at some points (1500x to 2400x). I know that
> >> this sequence should be there in the genome at different places with
> >> micro-heterogenity but it is assembled only as one contig and now i am
> >> not able to cover those remaining regions which are left as gaps due
> >> to this contig. Is there any way to grab the reads from the contig and
> >> reassemble them into several contigs with some accuracy?
> >>
> >> Or someone has better idea to resolve this case?
> >>
> >> Regards to all
> >> adnan
> >
> >
> >
>
> --
> Leonor Palmeira, PhD
>
> Phone: +32 4 366 42 69
> Email: mlpalmeira AT ulg DOT ac DOT be
> http://sites.google.com/site/leonorpalmeira
>
> Immunology-Vaccinology, Bat. B43b
> Faculty of Veterinary Medicine
> Boulevard de Colonster, 20
> University of Liege, B-4000 Liege (Sart-Tilman)
> Belgium
>
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