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

[Daniel Ence]

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]
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>
Sent: Friday, February 21, 2014 7:38 PM
To: Joseph Said
Cc: 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

________________________________________
From: Joseph Said [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