Est2Genome Problems

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Est2Genome Problems

Jason Gallant
Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756

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Re: Est2Genome Problems

Carson Holt-2
I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.

I’d like to at least have your test set to see if I can duplicate what you are seeing.

Use this to upload the job files then I can just run it from my server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson


On Feb 3, 2015, at 11:13 AM, Jason Gallant <[hidden email]> wrote:

Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Est2Genome Problems

chris H
Hi MAKER community,

I think I am seeing the same issue that Jason has reported. ran cufflinks, then cufflinks2gff3 and tried to feed the result to MAKER via 'est_gff=' with 'est2genome=1'. In the resulting gff file from maker I only get protein2genome and repeatmasker evidence. If I do a search in the maker log est2genome never comes up. Tried to extract the cufflinks results as fasta and feed to MAKER via 'est='. Still no indication that the evidence is used.

I am using MAKER 2.31.8. Any help would be much appreciated! Thanks in advance for your time!

cheers,
Christoph

On 10/02/2015 17:56, Carson Holt wrote:
I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.

I’d like to at least have your test set to see if I can duplicate what you are seeing.

Use this to upload the job files then I can just run it from my server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson


On Feb 3, 2015, at 11:13 AM, Jason Gallant <[hidden email]> wrote:

Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: Est2Genome Problems

Carson Holt-2
Jason never responded back to this one or uploaded his file to test. He probably figured it out off list. My guess is that your results are too fragmented to build a model that can pass filtering thresholds with.

If you want I can take a look. You can upload all files for a test job here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson



On Mar 7, 2017, at 5:51 PM, Christoph Hahn <[hidden email]> wrote:

Hi MAKER community,

I think I am seeing the same issue that Jason has reported. ran cufflinks, then cufflinks2gff3 and tried to feed the result to MAKER via 'est_gff=' with 'est2genome=1'. In the resulting gff file from maker I only get protein2genome and repeatmasker evidence. If I do a search in the maker log est2genome never comes up. Tried to extract the cufflinks results as fasta and feed to MAKER via 'est='. Still no indication that the evidence is used.

I am using MAKER 2.31.8. Any help would be much appreciated! Thanks in advance for your time!

cheers,
Christoph

On 10/02/2015 17:56, Carson Holt wrote:
I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.

I’d like to at least have your test set to see if I can duplicate what you are seeing.

Use this to upload the job files then I can just run it from my server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson


On Feb 3, 2015, at 11:13 AM, Jason Gallant <[hidden email]> wrote:

Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Est2Genome Problems

chris H
Dear Carson,

Thanks for getting in touch! I actually managed in the end. I converted the gtf I had from cufflinks to gff3 via the script 'gtf2gff.pl' from augustus and then used the script 'gffGetmRNA.pl' again from augustus to extract the mRNA in fasta. This file I fed to MAKER via the 'est=' route and now I get plenty of est2genome evidence in the maker result. So the problem seems to be limited to the route 'est_gff=', allthough there is no error message whatsoever the est2genome routine seems to never be triggered.

I'd still be happy to upload my data (the cufflinks gff, the genome fasta, anything else?) if you want to try to reproduce the problem. Let me know!

btw I seem to be unable to create a new topic or respond to topics via google groups. Is the list closed or the access restricted somehow. I only managed by responding to Jason's mail which I still had in my inbox directly via my gmail.

Thanks!

cheers,
Christoph

On 09/03/2017 19:39, Carson Holt wrote:
Jason never responded back to this one or uploaded his file to test. He probably figured it out off list. My guess is that your results are too fragmented to build a model that can pass filtering thresholds with.

If you want I can take a look. You can upload all files for a test job here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson



On Mar 7, 2017, at 5:51 PM, Christoph Hahn <[hidden email]> wrote:

Hi MAKER community,

I think I am seeing the same issue that Jason has reported. ran cufflinks, then cufflinks2gff3 and tried to feed the result to MAKER via 'est_gff=' with 'est2genome=1'. In the resulting gff file from maker I only get protein2genome and repeatmasker evidence. If I do a search in the maker log est2genome never comes up. Tried to extract the cufflinks results as fasta and feed to MAKER via 'est='. Still no indication that the evidence is used.

I am using MAKER 2.31.8. Any help would be much appreciated! Thanks in advance for your time!

cheers,
Christoph

On 10/02/2015 17:56, Carson Holt wrote:
I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.

I’d like to at least have your test set to see if I can duplicate what you are seeing.

Use this to upload the job files then I can just run it from my server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson


On Feb 3, 2015, at 11:13 AM, Jason Gallant <[hidden email]> wrote:

Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: Est2Genome Problems

Carson Holt-2
Sure. Send me the file. On a side note, I find cufflinks results to be very noisy (lot’s of false positives). I usually get better results using assembled reads from Trinity (with -jaccard_clip option set), or using Stringtie.

Thanks,
Carson


On Mar 10, 2017, at 1:50 AM, Christoph Hahn <[hidden email]> wrote:

Dear Carson,

Thanks for getting in touch! I actually managed in the end. I converted the gtf I had from cufflinks to gff3 via the script 'gtf2gff.pl' from augustus and then used the script 'gffGetmRNA.pl' again from augustus to extract the mRNA in fasta. This file I fed to MAKER via the 'est=' route and now I get plenty of est2genome evidence in the maker result. So the problem seems to be limited to the route 'est_gff=', allthough there is no error message whatsoever the est2genome routine seems to never be triggered.

I'd still be happy to upload my data (the cufflinks gff, the genome fasta, anything else?) if you want to try to reproduce the problem. Let me know!

btw I seem to be unable to create a new topic or respond to topics via google groups. Is the list closed or the access restricted somehow. I only managed by responding to Jason's mail which I still had in my inbox directly via my gmail.

Thanks!

cheers,
Christoph

On 09/03/2017 19:39, Carson Holt wrote:
Jason never responded back to this one or uploaded his file to test. He probably figured it out off list. My guess is that your results are too fragmented to build a model that can pass filtering thresholds with.

If you want I can take a look. You can upload all files for a test job here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson



On Mar 7, 2017, at 5:51 PM, Christoph Hahn <[hidden email]> wrote:

Hi MAKER community,

I think I am seeing the same issue that Jason has reported. ran cufflinks, then cufflinks2gff3 and tried to feed the result to MAKER via 'est_gff=' with 'est2genome=1'. In the resulting gff file from maker I only get protein2genome and repeatmasker evidence. If I do a search in the maker log est2genome never comes up. Tried to extract the cufflinks results as fasta and feed to MAKER via 'est='. Still no indication that the evidence is used.

I am using MAKER 2.31.8. Any help would be much appreciated! Thanks in advance for your time!

cheers,
Christoph

On 10/02/2015 17:56, Carson Holt wrote:
I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.

I’d like to at least have your test set to see if I can duplicate what you are seeing.

Use this to upload the job files then I can just run it from my server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi

—Carson


On Feb 3, 2015, at 11:13 AM, Jason Gallant <[hidden email]> wrote:

Hi Folks,

I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run.  I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files.  I even ran the accessory script gff3merge to check that the resulting file was properly formatted.

For options, I set est2genome=1 and est_gff=cufflinks.gff.  I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these.  Is there another option that I need to enable in order to use my est_gff file?  I’m trying to get a set of genes to train the predictors for my next step.

Any help would (as always) be greatly appreciated!

Best,
Jason Gallant


Dr. Jason R. Gallant
Assistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
office: 517-884-7756
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



_______________________________________________
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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
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