Gene Prediction Tools From Mapped Illumina Rnaseq Data Evidence?

Question

[Ahdf-Lell-Kocks]

What are the recommended tools to do gene prediction from mapped Illumina RNAseq data evidence? By gene prediction I mean the evidence-based definition of the transcripts for every coding and non-coding gene in the genome using mapped RNAseq reads. Also, can I use cufflinks if I have aligned the reads with BWA?

[Steve Lianoglou]

What do you mean by "gene prediction"? Are you trying to de novo assemble a transcriptome from RNA-seq data?

Answer 1

[Darked89]

For tophat mapped reads you can use cufflinks. I belive isolasso also uses mapped reads to reconstruct gene models.

If you want to go a bit more speculative, try Augustus.

[Leszek]

+1 for Augustus. In case of cufflinks, I have noticed often several genes close one to another appear as one transcript. At least in yeasts.

Answer 2

[Pasta]

If you want to annotate contigs of Prokaryotic origin you can use RAST