[mira_talk] Re: mira denovo assembly of solexa reads
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 17 Jan 2011 15:09:07 +0100
So I guess your expected coverage is probably extremely high... If your run
miramem (included in mira distribution), what does it tell you?
If it is over 70X, you may try to subsample your data, to aim at 50-70x
coverage and rerun mira.
HTH,
Lionel
On 17 janv. 2011, at 14:42, Saima Zubair <saim_zub@xxxxxxxxx> wrote:
> My expected genome size is about 2.1 to 2.2 MB. The version I am using is
> 3.2.0
>
> From: Lionel Guy <guy.lionel@xxxxxxxxx>
> To: mira_talk@xxxxxxxxxxxxx
> Sent: Mon, January 17, 2011 2:04:26 PM
> Subject: [mira_talk] Re: mira denovo assembly of solexa reads
>
> Hi Saima,
>
> What's your genome size (expected)? If you get very, very high coverage, you
> could have sky-high number of skims... (although 2^31 seems pretty big). What
> version of mira are you using?
>
> Cheers,
> Lionel
>
> On 17 Jan 2011, at 13:52 , Saima Zubair wrote:
>
> > Hi,
> >
> > I am doing the denovo assembly of solexa reads of 100 bps long. My data is
> > in the form of two mate_pair files, each file is of 3 GB. My assembly runs
> > strangely for more than a week and then following error occurs with
> > controlled program stop;
> >
> >
> > Internal logic/programming/debugging error (*sigh* this should not have
> > happened).
> >
> > "More than 2^31 skim hits would be taken ... this was not foreseen yet.
> >
> > ->Thrown: void Assembly::reduceSkimHits4(int32 version, const string
> > prefix, const string postfix, const string logname)
> > ->Caught: main
> >
> > Aborting process, probably due to an internal error.
> >
> > I have tried it with many different parameters but assembly is not complete
> > yet. Should I filter the data before running command?
> >
> >
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>
Other related posts:
