Hood Lab at ISB

RNASEQR-a streamlined and accurate RNA-seq sequence analysis program

System requirements

RNASEQR was written in Python 2.7, and shall run on most platforms as long as a Python interpreter (v2.7+) is installed. RNASEQR was developed on the 64-bit Cent OS Linux and shall run on both the 64- and the 32-bit Linux systems. RNASEQR has been tested on Bowtie v.0.12.7, BLAT v.34, Python 2.7, and shall theoretically work with newer versions.


To install Bowtie, BLAT, and Python, please check the developers’ websites.

Download the RNASEQR source codes (current version: 1.0.2) and decompress it to the directory of your choice.

# tar zxvf RNASEQR_v1.0.2.tgz

Running example dataset

Before analyzing your RNA-seq data using RNASEQR, please make sure you have properly installed RNASEQR and the required third party tools including Python (version 2.7 or later), Bowtie, and BLAT. To test drive RNASEQR, please download the following files.

  • Prebuilt BLAT index for human genome
  • Prebuilt Bowtie index for human genome
  • Prebuilt Bowtie index for human transcriptome (UCSC Known Gene HG19)
  • UCSC Known Gene annotation (HG19, BED format)
  • Test RNA-seq dataset and configuration files
  • To decompress these files, please enter

    # tar zxvf [file name].tgz

    The sample dataset is part of the RNA-seq data in database GEO with accession number GSE19166. There are two files which are paired-end; each file contains 10,000 RNA-seq sequence reads. The mapping/alignment result of the test dataset is available here.

  • Mapping/alignment result of the test dataset
  • The RNA-seq sequence files described in the RNASEQR manuscripts is available in database GEO with accession number GSE33328. Please read the manual for more information.

    Related Links

    Download dataset

  • MAQC test data
  • CCDS simulated data
  • Human GBM data
  • RNASEQR manuscript RNASEQR manual

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