Doing DEG for a suspected new transcript?

[SamCurt]

Hi all,

I have reviewed some of my mRNA-seq results and have noticed that both Scripture and Cufflinks' model reported a transcript located in my locus of interest and between two of our long-time candidate genes. I suspected the existence of lincRNA in play here.

However, this transcript has not been reported in any of the databases, and I would like to perform DEG analyses on this transcript as if it was a gene, using a count-based algorithm such as DESeq or DEGseq.

How should I edit the GTF files to perform counts on this transcripts (and its isoforms)?

Thanks in advance!