How to Annotate Long non coding RNA?

Question

[Hyper_Odin]

I am a bit confused about the annotation of Lnc-RNA. I have already downloaded the gencode gtf file and I i am using cufflinks, cuffmerge and cuffdiff. Aftercufflinks i get "transcripts.gtf" and at the end of cuffmerge i get "merged.gtf" Now i am not able to understand the next step. 1) At which file should I apply the cutoff filter of 200bp and then go for CPAT? is it the "transcript.gtf"? 2) If yes, then what will be the command to execute it?

I am reading several papers, but they have not described the procedure clearly! Thanks

Answer 1

[Nicolas Rosewick]

CPAT takes a fasta file in input and gives you an information if a transcript is coding or not . So you should first select the transcript of interest from your gtf then extract the sequence from the genome. Then CPAT

Answer 2

[27atcggcta27]

If I remember correctly, cuffmerge gives you a nonredundant list of transcripts between all your samples for you to use as the annotation later on. So I would apply the 200 nc cutoff here (merged.gtf) and then use CPAT. You could also use CNCI or CPC.