[mira_talk] Re: mira strain analysis caf files, and tracing the assemblies.
- From: Robin Kramer <kodream@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Mar 2011 18:33:32 -0600
That is what I thought, but I can't seem to find much assembly information
for this particular read in step2. It is in the step2_reads.caf file, but
there are no reads associated with it, to go back to step1. I was expecting
it to be in the step2_strainname directory, but it isn't in any of the caf,
fasta, or various info files either.
Sincerely yours,
Robin Kramer
On Wed, Mar 23, 2011 at 6:27 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Wednesday 23 March 2011 22:30:10 Robin Kramer wrote:
>
> > I am trying to trace an assembled contig back through the strain analysis
>
> > pipeline.
>
> >
>
> > When I convert the step3 assembly to an ace file and view it, I find a
>
> > contig that is supposedly from one of the strains, but when I look in the
>
> > corresponding strain's sequence and caf file in its step2 directory, I
>
> > don't find a contig with that name, though in the step2_straindata_in.txt
>
> > the name is there, and when I convert the step2_reads.caf to a fasta
> file,
>
> > the contig is there, but step2_reads.caf is incomplete, so I can't do
> much
>
> > with it.
>
> >
>
> > Is it possible to trace the reads in an assembly through the
> miraSearchEST
>
> > pipeline step1 through step3?
>
> Hmmm ... yes. Though what you describe lets me wonder a bit.
>
> Tracing a read in step 1 & 2 is trivial. It's the jump to step 3 which
> makes things a bit more complicated, but not much (I hope). Basically,
> taking the name of the contig of step2, you should find it in step3 as
> "read". Isn't this the case for your data?
>
> B.
>
>
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