Question: How to find Novel transcripts
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gravatar for williamsbrian5064
23 months ago by
williamsbrian5064230 wrote:

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

ADD COMMENTlink written 23 months ago by williamsbrian5064230

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 REPLYlink written 23 months ago by Amitm1.9k

Awesome links!! I appreciate the help!

ADD REPLYlink written 23 months ago by williamsbrian5064230
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