Ensembl GeneBuild pipeline. Annotate RNA-Seq data

Question

[GouthamAtla]

Hi, is there any documentation for GeneBuild pipeline to generate annotations (GTF) ? I could see it on github, but without documentation. I haf draft genome and around 150GB Rna-seq data. I would like to get annotations at isoform level, like that of standard Ensembl GTF file.

The other thing I could do is to run tophat2 --> cufflinks --> cuffmerge --> transcripts.gtf and try to annotate transcripts.gtf . Anybody annotated cufflinks generated gtf file ?

[Sam]

Can you perform cuffmerge with known transcript gtf? If so, then they should help you to annotate the known transcripts

[GouthamAtla]

cuffmerge for different libraries not with known gtf.

[GouthamAtla]

I got some link here: http://www.ensembl.org/info/genome/genebuild/2012_04_zebrafish_zv9_genebuild.pdf

Answer 1

[GouthamAtla]

This seems to be the pipeline. complicated.