Tophat using --no-novel-juncs

[genomicist]

I would like to align my reads to the annotated human transcriptome. One idea would be to use Tophat with the -G option supplying refFlat.gtf from UCSC and running in the --no-novel-juncs mode. Tophat then should construct junctions based on the GTF file. Does anyone know if actually the junctions are constructed joining exons following one after another, or will Tophat look at all possible junctions between exons?

Thanks.

[Jon_Keats]

I could be wrong but my interpretation was that it creates each junction defined by the TRANSCRIPTS in the gtf file. So for a gene with only one transcript you only have 1-2,2-3,3-4,4-5 junctions but if two transcripts exist one of which lacks exon 3 you get the aforementioned junctions plus 2-4 from the defined by the second transcript. It does not create all possible junctions 1-2, 1-3, 1-4, 1-5, 2-3, 2-4, 2-5, 3-4, 3-5, and 4-5. If you want that type of effect look at the Alexa-seq package

[genomicist]

Thank you for your reply. No, I do want only junctions that have evidence of existing transcripts.