[maker-devel] 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 <mjfi2sb3 at gmail.com>
Date: Tuesday, January 31, 2017 at 3:14 PM
To: Chris Fields <cjfields at illinois.edu>, Scott Cain <scott at scottcain.net>, Maya Britstein <mayabritstein at gmail.com>
Cc: "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>, "help at gmod.org" <help at gmod.org>
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, <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> 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 <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Scott Cain <scott at scottcain.net<mailto:scott at scottcain.net>>
Date: Wednesday, January 25, 2017 at 2:23 PM
To: Maya Britstein <mayabritstein at gmail.com<mailto:mayabritstein at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org> List" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>, "help at gmod.org<mailto:help at gmod.org>" <help at gmod.org<mailto:help at gmod.org>>
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 <mayabritstein at gmail.com<mailto:mayabritstein at gmail.com>> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_wiki_GFF3&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=OMPcIr8gCZc0MtV0NaCwpEmyn1zMeLOzW7v7LAyAcDU&s=B1gZmgsg06xIvtRwdOwnNvYzLU-obgTch1fU0jWhy9w&e=>)

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




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