[maker-devel] Maker example data for 2013 GMOD summer school

[Qihua Liang]

Hi Daniel,

Actually I'm blasting with both cowpea RNASeq and common bean RNASeq. And yes, the datasets are large, so it really takes me couple weeks by now and it's still on running. Do you have advices on fastening this process?

Thanks
Qihua

> On Apr 27, 2016, at 11:16 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Qihua, 
> 
> In the maker_opts.ctl file there is an option “cpus” which allows you to tell blast to use more than 1 cpu for blast. The comment for the line says that you should not set this higher than 1 when using MPI. I believe that the reason for this is that each thread runs blast on its own, so the number of cpus used will be the number of MPI threads X the number of cpus for blast, which can quickly get larger than the number of cpus available. 
> 
> At the same time, it’s usually not advisable to use tblastx to align large datasets because of the increased amount of time it takes. Are these RNAseq datasets from another species that you’re using tblastx for? 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
>> On Apr 27, 2016, at 12:06 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
>> 
>> Hi, Daniel
>> 
>> I am using Maker to annotate cowpea genome for a while but now I am wondering if I could use multi-threads instead of single one? It has been running tblastx for such a long time using single thread. But I couldn’t find such settings in documentations to assign multi-threads to run Maker. Is there such an option?
>> 
>> Thank you 
>> Qihua
>> 
>> 
>>> On Mar 30, 2016, at 2:17 PM, Daniel Ence <dence at genetics.utah.edu> wrote:
>>> 
>>> HI Qihua, 
>>> 
>>> I believe that most of the data we used in the tutorials are are available in the maker/data directory, which is included in all maker distributions. Please let me know if that isn’t the case. 
>>> 
>>> ~Daniel
>>> 
>>> 
>>> Daniel Ence
>>> Graduate Student
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> 
>>>> On Mar 30, 2016, at 3:10 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
>>>> 
>>>> Hi Michael and Daniel,
>>>> 
>>>> I am a graduate student in UC Riverside, and recently I am learning to use Maker for genome annotation. I was trying to find some tutorials to follow and practice on example data, and I found out that you were giving a talk on Maker during 2013 GMOD summer school and the tutorial of that is very detailed. Nice job!
>>>> 
>>>> But example data under the folder you mentioned as ./maker/maker_course is not provided on the website and I am wondering if they are available to the public or not. If yes, could you send me those materials so that I could follow your tutorial to practice using Maker?
>>>> 
>>>> Thank you
>>>> Best
>>>> Qihua
>