Re: GFF3 file format

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Re: GFF3 file format

Scott Cain
Hi Maya,

I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.

Scott


On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <[hidden email]> wrote:
Hi,

I have RNA-seq data, and genomic data that I want to annotate using maker. 

From what I understood, I need to genarate a gff3 file format from the RNA-seq mapping sequences. I had mapped the RNA sequences to the genome using bowtie and tophat. However, I still do not know how to take these format and convert them to a gff3 file that I can them use in maker as annotation evidence 

I saw the wiki page, that did not mention how to make this conversion (http://gmod.org/wiki/GFF3)

Can you please help me?

Sincerely,
Maya

----
Maya Britstein
Ph.D candidate
Laura Steindler's Lab
Marine Biology Department
Leon H. Charney School of Marine Sciences
University of Haifa, Israel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GFF3 file format

Fields, Christopher J
If I recall, from a BAM you would need to run a reference-based assembly on these data (e.g. Cufflinks2 or StringTie) to get this; you can also use Trinity for ref-based assembly.  But I always choose the route of a full de novo assembly (again, Trinity or similar) when possible, doing some basic cleanup (e.g. remove low confidence transcripts) and bring them as EST evidence.  

chris 

From: maker-devel <[hidden email]> on behalf of Scott Cain <[hidden email]>
Date: Wednesday, January 25, 2017 at 2:23 PM
To: Maya Britstein <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] GFF3 file format

Hi Maya,

I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.

Scott


On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <[hidden email]> wrote:
Hi,

I have RNA-seq data, and genomic data that I want to annotate using maker. 

From what I understood, I need to genarate a gff3 file format from the RNA-seq mapping sequences. I had mapped the RNA sequences to the genome using bowtie and tophat. However, I still do not know how to take these format and convert them to a gff3 file that I can them use in maker as annotation evidence 

I saw the wiki page, that did not mention how to make this conversion (http://gmod.org/wiki/GFF3)

Can you please help me?

Sincerely,
Maya

----
Maya Britstein
Ph.D candidate
Laura Steindler's Lab
Marine Biology Department
Leon H. Charney School of Marine Sciences
University of Haifa, Israel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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Re: GFF3 file format

Salim Bougouffa

Hi Christopher,

How would you identify a low confidence transcript? And how do you remove them? Also, did you try setting a minimum read coverage in Trinity as the default is one?

Best
/SB


On Thu, 26 Jan 2017, 01:04 Fields, Christopher J, <[hidden email]> wrote:
If I recall, from a BAM you would need to run a reference-based assembly on these data (e.g. Cufflinks2 or StringTie) to get this; you can also use Trinity for ref-based assembly.  But I always choose the route of a full de novo assembly (again, Trinity or similar) when possible, doing some basic cleanup (e.g. remove low confidence transcripts) and bring them as EST evidence.  

chris 

From: maker-devel <[hidden email]> on behalf of Scott Cain <[hidden email]>
Date: Wednesday, January 25, 2017 at 2:23 PM
To: Maya Britstein <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] GFF3 file format

Hi Maya,

I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.

Scott


On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <[hidden email]> wrote:
Hi,

I have RNA-seq data, and genomic data that I want to annotate using maker. 

From what I understood, I need to genarate a gff3 file format from the RNA-seq mapping sequences. I had mapped the RNA sequences to the genome using bowtie and tophat. However, I still do not know how to take these format and convert them to a gff3 file that I can them use in maker as annotation evidence 

I saw the wiki page, that did not mention how to make this conversion (http://gmod.org/wiki/GFF3)

Can you please help me?

Sincerely,
Maya

----
Maya Britstein
Ph.D candidate
Laura Steindler's Lab
Marine Biology Department
Leon H. Charney School of Marine Sciences
University of Haifa, Israel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
--

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Re: GFF3 file format

Fields, Christopher J

You can use RSEM for some initial filtering:

 

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification#filtering-transcripts

 

Then I generally use the Trinity QA steps, in particular TransRate or DETONATE:

 

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment

 

chris

 

From: Salim Bougouffa <[hidden email]>
Date: Tuesday, January 31, 2017 at 3:14 PM
To: Chris Fields <[hidden email]>, Scott Cain <[hidden email]>, Maya Britstein <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] GFF3 file format

 

Hi Christopher,

How would you identify a low confidence transcript? And how do you remove them? Also, did you try setting a minimum read coverage in Trinity as the default is one?

Best
/SB

 

On Thu, 26 Jan 2017, 01:04 Fields, Christopher J, <[hidden email]> wrote:

If I recall, from a BAM you would need to run a reference-based assembly on these data (e.g. Cufflinks2 or StringTie) to get this; you can also use Trinity for ref-based assembly.  But I always choose the route of a full de novo assembly (again, Trinity or similar) when possible, doing some basic cleanup (e.g. remove low confidence transcripts) and bring them as EST evidence.  

 

chris 

 

From: maker-devel <[hidden email]> on behalf of Scott Cain <[hidden email]>
Date: Wednesday, January 25, 2017 at 2:23 PM
To: Maya Britstein <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] GFF3 file format

 

Hi Maya,

 

I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.

 

Scott

 

 

On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <[hidden email]> wrote:

Hi,

 

I have RNA-seq data, and genomic data that I want to annotate using maker. 

 

From what I understood, I need to genarate a gff3 file format from the RNA-seq mapping sequences. I had mapped the RNA sequences to the genome using bowtie and tophat. However, I still do not know how to take these format and convert them to a gff3 file that I can them use in maker as annotation evidence 

 

I saw the wiki page, that did not mention how to make this conversion (http://gmod.org/wiki/GFF3)

 

Can you please help me?

 

Sincerely,

Maya

 

----

Maya Britstein

Ph.D candidate

Laura Steindler's Lab

Marine Biology Department

Leon H. Charney School of Marine Sciences

University of Haifa, Israel

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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

--

____________________________
Sent from Inbox Mobile


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[hidden email]
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