[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 2 Sep 2009 10:49:37 +0200
On Tue, Sep 1, 2009 at 9:00 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Dienstag 01 September 2009 Martin A. Hansen wrote:
> > I killed it - and zapped the directories - so I don't know :o(
>
> Ehmmm ... not good. But cannot be undone. I guess it should have been at
> least
> 80% done.
>
>
Or perhaps 99.9% :o) !!! How can you tell how far the process is?
> > Since this is a fairly simple genome, and the coverage is huge, I was
> > expecting it to run faster. Perhaps I am doing something wrong here:
> > mira -project=M1 -job=denovo,genome,normal,454,solexa
> > -GENERAL:number_of_threads=4 SOLEXA_SETTINGS -CO:msr=no
> > -GE:uti=no:tismin=2000:tismax=3000
>
> Nothing wrong. One might tune a few parameters to trade-off
> memory/run-time,
> but if your machine has only 16GB there's not much room.
>
> > Thurs we reduced the input reads from 3308974 to 2262531.
>
> Only reduced to 2/3? This seems a bit high. 70 contigs at 2 ends at 3kb per
> end is 420kb. Depending on your genome, this should represent between 1/5th
> and 1/20th of the overall genome size and correspondingly the reads should
> be
> reduced to a similar proportion.
>
>
The genome size of this bugger is ~3Mb. Thus the factor would be 1/7th,
true.
There is something weird going on with Bowtie. If using FASTA files (i.e. no
quality scores) I obtain 478352 hits mapping all reads to the contigs. Using
Solexa reads (including quality scores) I obtain 1287994 hits. If using
FASTA I guess the exercise will be futile because of too few mappable hits.
I could of cause try to improve this ...
Best regards,
Martin
> Regards,
> Bastien
>
>
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