1. Introduction
  2. 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.

  3. Compliation
  4. The source code contains two packages: graphlib and IsoInfer. To compile the source code, you should Note that it is necessary to keep the graphlib and isoinfer under the same directory. Environment variable LD_LIBRARY_PATH should be exported like the first step every time when you open a new shell to run the program. I suggest you putting it in the .bashrc file in your home directory.

  5. Manual
  6. 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.

  7. Reference
  8. Jianxing Feng, Wei Li and Tao Jiang. Inference of isoforms from short sequence reads. 2010. Accepted by RECOMB 2010.

  9. Questions and feedback
  10. Please email to: