transcript discovery using paired end read Illumina

[rodrigo.duarte88]

Dear folks,

I am quite new to RNAseq data analysis and would appreciate if anyone could guide me.

I am interested in simply finding out which transcripts of a single gene are expressed in a tissue we sent for sequencing. The problem is that we have RNAseq only from ONE sample. Is it still possible to run this type of transcript discovery?

(I mapped the paired end reads using tophat, and now am using cufflinks without a -g option)