Cuffnorm for normalisatioin of counts

Question

[Yaseen Ladak]

Hello All,

I am trying to use cuffnorm to normalise the counts. However, I am giving inputs as BAM files and I have the GTF obtained from ensembl. Do I need to use cufflinks as the first step to generate the GTF to be used with Cuffnorm or can I use the GTF that I have obtained from emnsebl for the genome to which I aligned the data?

I would be grateful for your advise?

Thank you Yaseen

Answer 1

[ablanchetcohen]

Use the Ensembl GTF file, unless you are interested in discovering novel transcripts that have not yet been annotated. If, and only if you are interested in discovering novel transcripts, you should run Cufflinks first to generate your own GTF annotation file, which you should then merge with the Ensembl GTF file. Otherwise, for well-annotated genomes, such as the human or the mouse genomes, it is not necessary to search for novel transcripts, since the majority of transcripts will already have been annotated, and will be present in the Ensembl GTF file.

Answer 2

[Yaseen Ladak]

Thank you very much really grateful for your support and this forum!