[mira_talk] Re: BAC vector sequece masking for de novo assembly using PacBio C2
- From: Juan Pascual Anaya <jpascualanaya@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 9 Dec 2013 09:33:20 +0900
Hi Bastien!
I've read that post and used -CO:mrpg=5... but I still have the same
problem with the megahubs. Should I keep using -SK:mmhr=5?? As I understand
from the manual, this is not very recommended, but without this, I don't
get MIRA to finish the assembly
Thanks!
Champi
On Sun, Dec 8, 2013 at 11:11 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 08 Dec 2013, at 13:16 , Juan Pascual Anaya <jpascualanaya@xxxxxxxxx>
> wrote:
>
> […]
> Now it's been running for a few hours without any complain, but I wonder
> how good is what I'm doing... My goal is to get those repeats also
> assembled, since they seem important for what I want to study (the Hox
> clusters of the hagfish; Hox clusters are usually repetitive
> sequence-free...).
>
> Any advices?
>
>
> You might be interested in a posting from a couple of days ago:
>
> //www.freelists.org/post/mira_talk/PacBio-data,4
>
> In your case, I’d go with -CO:mrpg=5 (or 6) as a first approximation.
>
> B.
>
>
--
Juan Pascual-Anaya, PhD
Research Scientist
Laboratory for Evolutionary Morphology
Center for Developmental Biology (CDB) RIKEN
2-2-3 Minatojima-minamimachi
Chuo-ku, Kobe, Hyogo 650-0047
Japan
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