How to find Novel transcripts
0
0
Entering edit mode
5.9 years ago

Hi,

I've asked a similar question to this before but I don't think I was descriptive enough. I had RNA-Seq done for me on a species that isn't studied very often. There is a reference genome so I have that to work with. The issue is that all the genes are predicted. I have had issues in the past where the predicted exons were completely off, so I have lost some respect for the predictions.

I was wondering if there was some kind of software that I could play with that might be able to pull out any novel transcripts and maybe even some novel isoforms. There are definitely a lot of programs that will map novel isoforms, but from what I have read, a lot of them require you to use the species transcriptome as a reference. Since I don't really trust this species transcriptome, I was wondering if there were any alternate methods? I have read paper about cufflinks but that seems rather out data?

Any help would be great!

Thanks

assembly alignment rna-seq next-gen • 1.6k views
ADD COMMENT
0
Entering edit mode

Have you seen here ? https://www.nature.com/articles/nbt.1883

There are other tools like Trinity, but its documentation is good and there are lots of downstream tools to play around with the assembled fasta.

ADD REPLY
0
Entering edit mode

Awesome links!! I appreciate the help!

ADD REPLY

Login before adding your answer.

Traffic: 1440 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