non coding rna in hordeum
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?
• 1,482 views
•
link
updated
by
dthorbur
•
written
by
martta95 •
•
written
by
martta95 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Plant transcriptome analysis and annotation
written by martta95 •
-
Protein annotation, gene annotation, hordeum vulgare RNA-Seq
written by martta95 •
-
KEGG adnotation
written by martta95 •
-
Gene ontology hordeum vulgare transcripts
written by martta95 •
-
Hordeum vulgare transcripts addnotation
written by martta95 •
-
Hordeum genes annotation
written by martta95 •
-
Regarding Barley genome
written by umeshtanwar2 •
-
Get CDS from consensus genome assembly
written by YocelynGG •
-
RNA-Seq and WGS analysis applied in genes expression
written by misterie
-
how to converting hordeum vulgare gene IDs (e.g. HORVU1Hr1G001920.3) to NCBI gene IDs?
written by arashzalnori •
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
I'm not looking for a genome I'm looking to find non-coding RNA in my RNA-Seq results
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
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.