[mira_talk] Re: MIRA: 454 reduced representation library
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 31 May 2010 19:41:49 +0200
On Montag 31 Mai 2010 Jens Carlsson wrote:
> I've got 454 sequences from a reduce representation library (restriction
> enzyme digested, the area from ~600-900 bp was extracted and used for
> the 454 without mechanically shearing the DNA)). Hence, I do not expect
> that the contigs should be very long and I therefore used the EST
> setting when assembling the sequences as to me the reduced
> representation data would look similar to EST, and got some 75K contigs
> (which to me makes sense). However, I also used the genome setting and
> got an order of magnitude fewer contigs...
> Would anyone know if I'm wrong using the EST settings?
I've never seen such data, so please take everything I say with a ton of salt.
Question is: is the number of reads in the contigs from with the genome
algorithms comparable? If not, you may perhaps want to rerun the genomic
version while switching off the propoesed end clipping (-CL:pec=no). -CL:pec
is very powerful, but not suited for low-coverage data as I presume yours is.
Might be it's throwing away way to much.
When --job=est is used, -CL:pec is off by default, while --job=genome turns it
on by default.
Regards,
Bastien
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