Illumina has generously provided a set of freely downloadable packages that contain everything you need to get started working with TopHat and Cufflinks. These packages contain Bowtie indexes for the human, mouse, and fly genomes as well as many others. The packages also contain annotation files (in GTF format) from UCSC, Ensembl, NCBI, and other sources. These files are augmented with the special attributes Cufflinks needs to perform differential splicing and promoter analysis. We strongly encourage users to download and try these packages!