[mira_talk] Re: fosmid assembly using mira
- From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Dec 2009 13:04:54 +0100
great! will give it a try...
On Wed, Dec 23, 2009 at 12:59 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> On Mittwoch 23 Dezember 2009 Rohit Ghai wrote:
> > thanks a lot for the new links. The usage is clear in the manual. I am
> > currently working with MIRA V3rc1 (aka 2.9.48). so the ssaha2 is already
> > being used in this version or do I have to install the one you have
> > suggested ?
>
> Take the last one, it's not yet present in rc1.
>
> > Regardless of your comment that the paired-end section would not help, it
> > did help a bit in that I realised that I needed to have qual and
> traceinfo
> > files for my sanger data, which is essentially the ends of the fosmids we
> > sequenced. I have only fasta files (no qual etc) ,can I use dummy qual
> > files ? ( say with a constant quality score of say 40).
>
> If none of your Sanger files has qualities, you do not need to generate
> fake
> ones.
>
> Instead, turn of "wants quality file", set the default quality for Sanger
> settings to any value you like.
>
> SANGER_SETTINGS -LR:wqf=no -AS:bdq=40
>
> > I hope the format is alright.
>
> If MIRA reads it, then it should be ok.
>
> B.
>
> --
> 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:
