About Read-Split-Run

What is RSR?

A computational method for identifing non-canonical, possibly very short, splicing regions using RNA-Seq data. The pipeline takes in RNA-Seq data in FASTQ format, utilizes BOWTIE (Langmead B, Trapnell C, Pop M, Salzberg) to align the sequences to the genome of your choice, splits the aligned reads, re-aligns them, then performs a sequence of filters to output a table of matched reads and the genes they belong to (or not).


  • Read the initial paper for Read-Split-Walk here.

  • The speedups attained between the initial release of Read-Split-Walk and the pending release has prompted a change of name to "Read-Split-Run".

  • RSR is freely available for academic purposes (under Apache License 2.0, see the LICENSE in the software package). RSR software can be downloaded at the github repository for RSR: https://github.com/xuric/read-split-run. To install the software on your system, download the zip file from the github repository and follow the instructions in the README file after you unzip.

    To verify your installation, you can download sample data files from our server. To download the sample mm9 mouse data files, click here; the file is a 753MB .zip file. After uncompressing, you will have two sample data files to test. You will also need to download from here the bowtie and refFlat files mentioned in the README contained in our software package; this file is a 2.4GB .zip file. After uncompressing, you should check the README contained in the software package to see where to put the bowtie and reflat files. You will know the pipeline is running properly if (1) the results for the Het sample include a splice in the Xbp1 gene that is 26 bp long, and (2) the results for the KO sample does not include the same splice.