Gene Prediction Tools From Mapped Illumina Rnaseq Data Evidence?
2
2
Entering edit mode
12.3 years ago
Ahdf-Lell-Kocks ★ 1.6k

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 • 3.5k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
12.3 years ago
Darked89 4.6k

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.

ADD COMMENT
0
Entering edit mode

+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.

ADD REPLY
2
Entering edit mode
12.3 years ago
Pasta ★ 1.3k

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

ADD COMMENT

Login before adding your answer.

Traffic: 2106 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6