RNASEQR source codes are now moved to the RNASEQR page at Institute for Systems Biology, please visit
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RNASEQR - A streamlined and accurate RNA-seq sequence analysis program 

RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of the annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results. 

Please note that RNASEQR requires Python 2.7 or later. If you have an older version, please upgrade your Python or contact your system administrator. 

The source codes have been primarily built for analyzing human RNA-seq datasets using the ENSEMBL gene annotation. If you plan to run the datasets of other species, please execute "non_human.pl" after concatenating nucleotide sequences of each chromosome.  

===  Obtain RNASEQR  ===
The source codes at github are now moved to a dedicated RNASEQR page at Institute For Systems Biology. Please visit http://hood.systemsbiology.net/rnaseqr.php to download the latest RNASEQR source codes and user manual.

===  Citing RNASEQR  ===
RNASEQR - A streamlined and accurate RNA-seq sequence analysis program
Leslie Y Chen, Kuo-Chen Wei, Abner C.-Y. Huang, Kai Wang, Chiung-Yin Huang, Danielle Yi, Chuan Yi Tang, David J. Galas, Leroy E. Hood
Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr1248

===  LICENSE  ===
RNASEQR is distributed under the GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007