[mira_talk] Re: Maximum read length.
- From: Andrzej N <andrzej.k.n@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 9 Jul 2010 01:31:51 -0500
Hello Bastien,
Thank you for advice about GTAGDB now it's working, I couldn't find out how
to make it to work. THANK YOU.
I have additional question... my sample is quite "polymorphic"... and
because of that I have so many contigs which are basically different between
each other because of ONE SNP (sometime 2-4bp difference)... Can I ignore
that? I would like to try make a "draft" do build genome and than work on
that kind of "small" thinks. This is making building whole genome quite
difficult...
Andrzej
On Sun, Jun 27, 2010 at 3:55 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Donnerstag 24 Juni 2010 Andrzej N wrote:
> > [...]
> > BTW. Can you please look at attachment, there is some issue with contigs
> > joining. I edit this "by hand" but...
> >
> > Settings:
> >
> > ./mira -project=moje2 -job=denovo,genome,accurate,454 -highlyrepetitive
> > -SK:mnr=yes:not=3 -SB:abnc=yes -AS:mrl=60:ardct=100
>
> Which version of MIRA is that? Current versions will not accept this
> command
> line anymore. Please use either 3.0.5 or, if you want, the current
> development
> version 3.1.15 which should also fix cases like the one you showed in the
> screenshot.
>
> Additionally, -SB:abnc=yes has no effect in de-novo assemblies.
>
> Additionally, I see that you are not using gap4 / MIRA to the fullest
> extend
> as you haven't told gap4 about the MIRA tags. Append the file GTAGDB from
> the
> MIRA distribution (.support/GTAGDB) to the GTAGDB file of your gap4
> installation ($STADENROOT/tables/GTAGDB) and restart gap4. Then you will be
> able to search for all places MIRA has doubts by searching, e.g., SRMc or
> IUPc
> tags.
>
> B.
>
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