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.
Thanks.
Comment