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Gene Prediction Tools From Mapped Illumina Rnaseq Data Evidence?

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?

illumina rna gene
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updated by Pasta • Pasta • written by Ahdf-Lell-Kocks • Ahdf-Lell-Kocks

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

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written by Steve Lianoglou Steve Lianoglou

2 answers

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.

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written by Darked89 Darked89

+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.

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written by Leszek Leszek

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

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written by Pasta • Pasta

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