[mira_talk] Re: How many passes to use.....
- From: Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 20 Nov 2013 12:25:11 +1000
Hi all,
Going back to the number of passes.
I have recently assembled a BAC from 454 single end reads. I expected that
by increasing the number of passes, the number of contigs would increase as
well since mira would learn from the repeats it found and split contigs
that may have been missassembled. However, I was surprised to find that
mira actually did not split the contigs, but joined them and increased the
largest contig size from 14Kb in nop=6 to 23Kb in nop=7.
When I increased nop to 8, the largest contig was split back again to 14Kb
long.
Is this normal behaviour? I must admit that the reads are kind of crappy.
They were badly clipped and I could not see the sff file, just the fastq
files. Anyway I let mira do its own clipping being careful enough to clip
vectors in the 5' end of the reads.
Cheers,
Juan Montenegro
2013/11/15 Bastien Chevreux <bach@xxxxxxxxxxxx>
> On 14 Nov 2013, at 16:47 , Torben Nielsen <torben@xxxxxxxxxx> wrote:
> >> Whether you assemble the metagenome data in genome or EST mode would
> have been
> >> interesting.
> > It's done in genome mode. Do you see any advantage to treating it as EST?
>
> Metagenome data being really “special”, there are pros and contras for
> both modes. Depending on what I’m looking for, I sometimes do both.
>
> B.
>
>
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