[mira_talk] Re: mira strain analysis caf files, and tracing the assemblies.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 24 Mar 2011 01:27:22 +0100
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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