[mira_talk] Re: MIRA: I am doing it wrong.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 4 Dec 2009 21:10:38 +0100
On Freitag 04 Dezember 2009 Alessandro Riccombeni wrote:
> The sequencing service provided a preassembled dataset as well: 39
> scaffolds and 933 contigs.
Ummm ... 933 contigs in Newbler versus 11000 in MIRA. Something is wrong
there.
> Some info: 13 Mbs, 2.38% are Ns, GC in the sequence is 36%, largest
> scaffold is 1.9 Mb and the smallest is 3Kb.
> After my first MIRA run with the 454 only (as they shouldn't have used any
> non-454 reads) I was quite clueless about which strategy did they use to
> get 39 scaffolds where I got 11000 contigs. As I wrote, they didn't use
> any custom adaptor, so I don't know what I should do as preprocessing
> goes...
Titanium paired-end ... did you use the two Titanium linker sequences in
sff_extract?
Regards,
Bastien
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