I am a novice of RNA-Seq analysis. For differentially expressed genes anaysis, I am trying to run bowtie/tophat and cufflinks pipeline with own transcriptome as a reference. Can I run with only the transcriptome without GTF file? My species is salmon that there is no genome for GTF file. Is the GTF file essential for this pipeline?
Thank you in advance for any idea and suggestion for this fundimental question.