Ncrna in cufflink analyzed RNA-seq

Question

[kanwarjag]

I ran RNA- seq analysis through cufflink to cuff diff . I looked in various files but could not see lincRNA/ ncRNA any suggestion in which file I should be looking them

Thanks

Answer 1

[Kevin Blighe]

They will be there but perhaps not with IDs that you'd expect. A ncRNA is the same as a coding RNA but just one that's not translated into a protein. There is no distinction between these at the genomic or transcriptomic levels; thus, they will not specifically be marked as lincRNAs, etc. However, you may infer them by the fact that they will have a single exon.

I would re-run TopHat/Cufflinks using a comprehensive GTF guide that includes, along with coding mRNAs, all 'known' ncRNAs, such as that provided by GENCODE (direct link; unpack this with gzip when downloaded) (source: http://www.gencodegenes.org/releases/current.html).

If you want to copy/paste part of your results from Cufflinks (such as transcripts.gtf), then I would be happy to take a look here.

Others will have other suggestions.