non coding rna in hordeum

Question

[martta95]

hello, I have RNA-seq results and I have sequences mapped to reference genome Hordeum vulgare. I would like to find a non coding RNA, which program I can use?

[Jack Tierney]

Are you looking for a specific RNA? If so you will need an annotation for this genome and then you can get the number of reads that map to each transcript.

If you would like to identify new ncRNAs then you might need to choose a different tool depending on the type of ncRNA

[martta95]

I'm not looking for a genome I'm looking to find non-coding RNA in my RNA-Seq results

[Jack Tierney]

Yes, I know haha I think you may be looking to see existing annotated ncRNAs. You can find them in a genome annotation which essentially is a file that details where features, such as non coding RNAs, are encoded in the genome. I can see from the similar posts section that GenoMax already showed you how to get an annotation on a similar question in the past.

Once you have an annotation you should consider a tool like RSEM to quantify annotated transcripts

[dthorbur]

You could also do a de novo transcriptome assembly of RNA not in the existing annotations using StringTie. It would be up to you to determine whether these additional transcripts are non-coding or not.