Annotating Cufflinks GTF with Maker

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Annotating Cufflinks GTF with Maker

Goutham atla
Dear All,

I have a draft genome for organism of my interest and I have around 150G of 100bp paired-end RNA-Seq data from different conditions. This organism has ensemble annotations but very few.

My goal is to look at differential splicing analysis between two conditions. For this I need good annotations in gtf format at isoform level.I am interested in using the Splicing Analysis Kit

For now, I have aligned one sample to genome using tophat2 and then used cufflinks to generate a de-novo GTF file. In either cases I have not used the avail be GTF with very few annotations.

The GTF file generated by cufflinks should be annotated to know the function of each transcript. So I am interested in adding annotations to the gtf file generated from cufflinks. What is the best of doing it ?

Or is there any better way of getting a gtf file, like that of ensemble, from my data ?

I have looked at trinotate, but its more about functional annotation and expression studies.


Regards,

--
Goutham Atla

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Re: Annotating Cufflinks GTF with Maker

Carson Holt-2
MAKER and it’s tools works with GFF3 format.  The same is true of most GMOD tools.  If you want to write your own parser, you can try using bioperl to covert back and forth between GTF (which is GFF2) and GFF3.  There may be a number of other tools that you can find by googling that can do this conversion.  Most of what you are describing might actually be easier to do in GFF3 format using GMOD tools (http://gmod.org/wiki/Main_Page).

You can try and use blast to identify putative functions of a gene by copying functions from another annotated genes, but you will probably have to build your own parser.  Your goals are specific enough that you will likely have to develop your own scripts to do parts of what you want.

—Carson


On Mar 27, 2015, at 11:37 PM, Goutham atla <[hidden email]> wrote:

Dear All,

I have a draft genome for organism of my interest and I have around 150G of 100bp paired-end RNA-Seq data from different conditions. This organism has ensemble annotations but very few.

My goal is to look at differential splicing analysis between two conditions. For this I need good annotations in gtf format at isoform level.I am interested in using the Splicing Analysis Kit

For now, I have aligned one sample to genome using tophat2 and then used cufflinks to generate a de-novo GTF file. In either cases I have not used the avail be GTF with very few annotations.

The GTF file generated by cufflinks should be annotated to know the function of each transcript. So I am interested in adding annotations to the gtf file generated from cufflinks. What is the best of doing it ?

Or is there any better way of getting a gtf file, like that of ensemble, from my data ?

I have looked at trinotate, but its more about functional annotation and expression studies.


Regards,

--
Goutham Atla
_______________________________________________
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