![]() Take note of the boost installation directory, because you will need to tell the Cufflinks installer where to find Boost later on. The default Boost installation directory is /usr/local. Note that you can specify where to put Boost with the -prefix option. This directory is called the BOOST_ROOT in some Boost installation instructions. Unpack the Boost tarball and cd to the Boost source directory.The issue is expected to be fixed in the upcoming Boost v1.59. WARNING: Due to a serious issue with Boost Serlialization library introduced in version 1.56, Cufflinks currently can only be built with Boost version 1.55 or lower. Download Boost and the bjam build engine.See below for instructions on installing Boost. In order to build Cufflinks, you must have the Boost C++ libraries (version 1.47 or higher) installed on your system. To use the binary packages, simply download the appropriate one for your machine, untar it, and make sure the cufflinks,cuffdiff and cuffcompare binaries are in a directory in your PATH environment variable. In order to make it easy to install Cufflinks, we provide a few binary packages here to save users from the occasionally frustrating process of building Cufflinks, which requires that you install the Boost libraries. To get the latest updates on the Cufflinks project and the rest of the "Tuxedo tools", please subscribe to our mailing list Install quick-start Installing a pre-compiled binary release The project is now maintained by Cole Trapnell's lab at the University of Washington.Ĭufflinks is provided under the OSI-approved Boost License News Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.Ĭufflinks was originally developed as part of a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. NOTE: If you're looking for old releases of Cufflinks, including source, you can find them here.Ĭufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
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