[maker-devel] I am a PhD candidate at NMSU and have a question about maker2

Sat Feb 22 16:21:51 MST 2014

Hi Hua, will you upload the genome file to this URL?
http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=170
I am more concerned that MAKER didn't find the gene in the whole genome than in the 60bp substring. I think that MAKER needs more sequence than that to annotate a gene model.

Will you also upload the MAKER output and datastore from the MAKER run?

Thanks,
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
________________________________
From: Hua Zhong [zh9118 at gmail.com]
Sent: Saturday, February 22, 2014 4:00 PM
To: Daniel Ence
Cc: maker-devel at yandell-lab.org; Joseph Said; Joe Song
Subject: RE: I am a PhD candidate at NMSU and have a question about maker2

The long file we used is a whole genome. Quite huge a file. I am not able to send that. Sorry. But in the simple test i told you, the nucleotide sequence sent you is consider to be the genome file, and protein sequence is another input. There two are what we want to blast against to each other to see if Maker2 works well.
Thanks.

On Feb 22, 2014 3:51 PM, "Daniel Ence" <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>> wrote:
Hi,

Will you send me the long file that you were trying to blast against?

Thanks,
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
________________________________
From: Hua Zhong [zh9118 at gmail.com<mailto:zh9118 at gmail.com>]
Sent: Saturday, February 22, 2014 10:46 AM
To: Daniel Ence
Cc: Joe Song; Joseph Said
Subject: Re: I am a PhD candidate at NMSU and have a question about maker2

hi all,
Attached are the three configuration files and two input files, which are used to predict something between the genome and protein. For a simple test, we used one short sequence about 60bp and its translated protein sequence as inputs. But got nothing returned. What's more, we did test long genome sequence as one input as well, but still got nothing. I am not sure what's the reason cause this result.
Thanks a lot for help.

Hua

On Fri, Feb 21, 2014 at 9:31 PM, Joseph Said <joesaid at nmsu.edu<mailto:joesaid at nmsu.edu>> wrote:
Hi Daniel,

I do not have the exact files with me right now, but my coauthors on the paper I am working on have been copied on this email. Hua can send you those files. Thank you for being very helpful especially on a Friday night.

Thanks,
Joe

Sent from my iPad

> On Feb 21, 2014, at 9:27 PM, "Daniel Ence" <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>> wrote:
>
> Hi Joe,
>
> MAKER runs blast from your local system (or your server where MAKER is installed), and it blasts evidence that the user supplies in the "est" and "protein" settings. The est and protein settings are set in the maker_opts.ctl file. The path to blast is set in the "maker_exe.ctl" file and the specific blast settings are in the "maker_bopts.ctl" file.
>
> Will you attach those file to your reply, so we can make sure that the settings are set up correctly?
>
> Thanks,
> 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
> ________________________________________
> From: Joseph Said [joesaid at nmsu.edu<mailto:joesaid at nmsu.edu>]
> Sent: Friday, February 21, 2014 7:44 PM
> To: Daniel Ence
> Subject: RE: I am a PhD candidate at NMSU and have a question about maker2
>
> Hi Daniel,
>
> Thank you for getting back to me so quickly. I am using the cotton Gossypium raimondii D genome from NCBI, and the arabidopsis gene is the GUN1 gene with ID UGID:8241, UniGene At.20815. I am using Maker2, and I believe maker2 just calls BLAST from NCBI's page. So when I search the cotton genome it returns zero hits. But then I used a known cotton gene as a test and ran a search and also returned zero hits. I am not sure what the problem is but it seems like the protocol that should be returning the results of NCBI's BLAST is returning 0 to Maker2 which is reporting 0 hits. I can a BLAST standalone and came up with hits for both my gene of interest and the control test gene and came up with results.
>
> Thanks,
> Joe
> ________________________________________
> From: Daniel Ence <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>>
> Sent: Friday, February 21, 2014 7:38 PM
> To: Joseph Said
> Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
> Subject: RE: I am a PhD candidate at NMSU and have a question about maker2
>
> Hi Joe,
>
> Will you upload your control files and data at this URL?
> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=169
>
> Also, what version of MAKER and blast are you using? And which file are you using for the known arabidopsis gene?
>
> I've copied this email to the maker-development list, which is a really good resource for trouble-shooting MAKER issues.
>
> Thanks,
> 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
> ________________________________________
> From: Mark Yandell
> Sent: Friday, February 21, 2014 7:32 PM
> To: Daniel Ence
> Subject: FW: I am a PhD candidate at NMSU and have a question about maker2
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707<tel:801-587-7707>
>
> ________________________________________
> From: Joseph Said [joesaid at nmsu.edu<mailto:joesaid at nmsu.edu>]
> Sent: Friday, February 21, 2014 5:18 PM
> To: Mark Yandell
> Subject: I am a PhD candidate at NMSU and have a question about maker2
>
> Dear Dr. Yandell,
>
> I am a molecular biologist at NMSU. I am trying to use maker2 with the cotton genome, and search an Arabidopsis gene against it. I think there is a problem with the blast component because zero results are returned. I tried troubleshooting by searching a known gene and still returned zero results. Is this a common problem maybe with the pipeline? I would appreciate any ideas you might have to help me.
>
> Thank you,
> Joe
>
> Sent from my iPad

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140222/0033879e/attachment-0003.html>