How to find Novel transcripts
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6.6 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 • 1.7k views
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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.

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Awesome links!! I appreciate the help!

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