IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. The source code is provided for non-commercial usage. We appologize for the unavailability of the Windows and Mac versions of this program at the present time.
Install the following C/C++ libraries: glpk, gsl and QuadProg++. If you
cannot install those packages in the standard system directories but
install them at "/your/installed/path/" for example, you have to modify the
environment variables LD_LIBRARY_PATH and CXXFLAGS by :
$ export CXXFLAGS="-I/your/installed/path/include -L/your/installed/path/lib"
$ export LD_LIBRARY_PATH="/your/installed/path/lib:"$LD_LIBRARY_PATH
Compile the graphlib package in the source code. The compilation follows the standard
configure, make process by execute the following commands in sequence:
$ ./configure
$ make
Compile the isoinfer package in the source code. The compilation follows the standard
configure, make process by execute the following commands in sequence:
$ ./configure
$ make
The usage of this program is contained in the executable file. We also provide three example files needed by IsoInfer at the first step. These files store the exon-intron boundaries, TSS/PAS pairs and gene range information extracted from UCSC mm9 knownGene table. A simple example script is also provided.
Jianxing Feng, Wei Li and Tao Jiang. Inference of isoforms from short sequence reads. 2010. Accepted by RECOMB 2010.
Please email to:
feeldead
TA
gmail.com