The Tophat2 entry screen does not list the reference genomes, however Bowtie2 does list them ( the ones I have in the bowtie2_indices.loc). The bowtie2_indices.loc states that this file works for both Bowtie2 and Tophat2. -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research and Geospatial Technology Services Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu