[maker-devel] 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
<http://cbcb.umd.edu/software/spanki/>

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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