[mira_talk] Re: fosmid assembly using mira
- From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 10 Jan 2010 15:33:12 +0100
Thanks Bastien.. I will rename the reads accordingly and try again
cheers
Rohit
On Sun, Jan 10, 2010 at 2:49 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Mittwoch 23 Dezember 2009 Rohit Ghai wrote:
> > Hi
> >
> > I am trying a sort of hybrid assembly. Though the mate-pairs are only in
> > fasta files ( all of them in the same file ).. I have no scf for these
> > files. I have generated sanger traceinfo file that looks like this..below
> > is one mate-pair ( different trace_names but same template_id )
> > [...]
> > Mira seems to run nicely but I saw the following in the output
>
> Hi Rohit,
>
> that's because the naming of your reads does not follow any read naming
> standard I know (or MIRA, which knows Sanger, TIGR, St.-Louis,
> Forward/Reverse
> and Solexa).
>
> Have a look at your read names:
>
> > <trace_name>AFD0ABA46ZH08FM1</trace_name>
> > [...]
> > <trace_name>AFD0ABA46ZH08RM1</trace_name>
>
> The closest youtr naming scheme comes to is the Forward/Reverse naming
> scheme,
> but the your names should be:
>
> > <trace_name>AFD0ABA46ZH08.FM1</trace_name>
> > [...]
> > <trace_name>AFD0ABA46ZH08.RM1</trace_name>
>
> More info on read naming schemes is in the MIRA docs for the "-LR:rns"
> parameter.
>
> Regards,
> Bastien
>
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