[maker-devel] 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, <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> on behalf of
> Scott Cain <scott at scottcain.net>
> Date: Wednesday, January 25, 2017 at 2:23 PM
> To: 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 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>
> 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
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=OMPcIr8gCZc0MtV0NaCwpEmyn1zMeLOzW7v7LAyAcDU&s=wb5XMrtNYBOrAngXKEi9GdfppioFQ3nnLiJvcdP1jLo&e=>)
>                    216-392-3087
> Ontario Institute for Cancer Research
>
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