Prep_reads filters out mappings whose read ID is NOT found in the flt_reads file, and write them into aux_outfile; also reverses the flt_reads filter itself
Parent program: tophat
TopHat is a fast tool for splice junction mapping for RNA-Seq reads. It aligns reads to genome using the high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. It can work without a reference annotation and process mammalian-sized genomes.