Using RNA seq for genome annotation

Question

[Picasa]

Hi,

I would like to provide rna seq evidence to Maker for genome annotation.

For the transcriptome building, I have done a reference based assembly with STAR+cufflinks but I am not sure if it is the correct way,

Do you have some experience with this ?

[Ben]

Do you want to annotate the genome?

[Picasa]

yes, and i want to provide rna seq evidence

[Ben]

RNA-seq evidenece? I do not understand what you want to express

[Picasa]

Well Maker needs (not mandatory but recommended) transcriptome to infer gene with gene predictor.

Answer 1

[sagnik]

Hello,

We have developed a gene annotator called FINDER which can annotate eukaryotic genomes using short-read RNA-Seq reads and protein sequences. It is completely automated and requires no manual intervention. FINDER also runs BRAKER to incorporate predicted genes in the repertoire. You can access the paper from FINDER and the software from here GitHub.

Thank you.

[jared.andrews07]

You might consider making a "Tool" post for this so that it is easier to find and you can more fully explain its capabilities.

[Istvan Albert]

Please do not post this exact same content over and over again. It is not how the site is supposed to work, we are not a billboard for posting a tool into every single potentially appropriate thread..