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TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the Institute of Genetic Medicine at Johns Hopkins University, the Department of Mathematics at the University of California, Berkeley, and the Department of Stem Cell and Regenerative Biology at Harvard University. See http://tophat.cbcb.umd.edu for more information. Notes on compiling the package from source: ------------------------------------------- TopHat requires the Samtools package (http://samtools.sourceforge.net/) in order to generate and handle the compressed, binary alignment files (BAM). The --with-bam=<bam_prefix> option of the configure script expects the following subdirectories and files: <bam_prefix>/include/bam/*.h (all the header files from Samtools) <bam_prefix>/lib/libbam.a (obtained by compiling Samtools) At the time of this writing the Samtools package does not have an install routine the user will have to explicitly create the above directory structure (./include/bam/ and ./lib) and copy the required Samtools files as indicated (the header files and libbam.a)