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 ?