Cufflinks transcript.gtf single exon entries

[ashish_yeri]

Hi all,

How many exons have to covered in a transcript for Cufflinks to annotate that as a transcript? I noticed that some entries in the cufflinks transcript.gtf file contain only the Ensembl gene ID. These are entries for which only a single exon has been mapped and assembled. Here, the Ensembl gene ID is given in place of the Ensembl transcript ID. Does this mean that for transcripts where all exons are not covered, Cufflinks does not provide an Ensembl transcript ID, but just annotates the Ensembl gene ID only?

I have included the part of the output of my transcript.gtf file:

1 Cufflinks transcript 139790 140339 113 - . gene_id "ENSG00000239906.1"; transcript_id "ENSG00000239906.1"; FPKM "1.3118385634"; frac "0.158204"; conf_lo "0.000000"; conf_hi "2.764030"; cov "2.093546";
1 Cufflinks exon 139790 140339 113 - . gene_id "ENSG00000239906.1"; transcript_id "ENSG00000239906.1"; exon_number "1"; FPKM "1.3118385634"; frac "0.158204"; conf_lo "0.000000"; conf_hi "2.764030"; cov "2.093546";

Any help will be greatly appreciated.

Thanks,

Ashish