Question: Ncrna in cufflink analyzed RNA-seq
gravatar for kanwarjag
9 weeks ago by
United States
kanwarjag830 wrote:

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


rna-seq • 194 views
ADD COMMENTlink modified 9 weeks ago by Kevin Blighe9.3k • written 9 weeks ago by kanwarjag830
gravatar for Kevin Blighe
9 weeks ago by
Kevin Blighe9.3k
Kevin Blighe9.3k wrote:

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:

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.

ADD COMMENTlink written 9 weeks ago by Kevin Blighe9.3k
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