[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: Tue, 10 Dec 2013 22:36:12 +0900
Hi there,
Sorry to keep bugging with this, but my e-mail was probably overlooked in
between so many questions about the mira3... XD
As an update on my playing with MIRA4 (4rc5 now), I can't play with
-CO:mrpg since I cannot get the MIRA to start the assembly. Also, my
problems don't come out from being particularly PacBio data, but for the
repetitive elements. And thus I always get some percentage of megahubs
between 1-5%. For some reason, after reading the manual and the output of
the MIRA abortion, I am sort of scared to increase the -SK:mmhr... although
I have seen in other posts that it can be set to 100 if one wants the
repeats also assembled... like in my case (so I should use then
-HS:mnr=off). I have tried to play with -HS:nrr too, but with no luck.
So, increasing the megahub ratio, although the assembly can take much
longer, is a good solution to get the BACs assembled?
Thank you in advance!
Champi
On Mon, Dec 9, 2013 at 9:33 AM, Juan Pascual Anaya
<jpascualanaya@xxxxxxxxx>wrote:
> 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
>
--
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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