The integrated software to manage and analysis next generation sequencing pipeline.(v1.0.2,11-4-2014)

Latest News

StringTie has been added in the pipeline as a optional choice of assemble step.

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.


RNAfinder is a collection of command line programs for unix-style operating systems written in Python2 and R. Running this pipeline need python2.7 and R environment.

Quick Start

Run RNAfinder from the command line like this:

python ./RNAfinder.py [config_file] [start] [end]


python ./RNAfinder.py ./config.txt all  #'all' means run all modules
python ./RNAfinder.py ./config.txt 1 4 #only run the module 1 2 3 and 4
python ./RNAfinder.py ./config.txt 4 4 #only run the module 4

User Guide

The main input of the pipeline is the config file.
Download the sample config file.

The module list of RNAfinder is as follow:

  • m1_QC
  • m2_mapping
  • m3_assemble
  • m4_different expression
  • m5_feature caculation
  • m6_RNA filter and annotation
  • m7_basic analysis
  • m8_function analysis
  • m9_alternative splicing
  • m10_miRNA target prediction
  • m11_tissue/condition specificity
  • m12_co-expression network
  • m13_ceRNA network

Usage of the RNAfinder pipeline:

  1. Prepare for running the pipeline:

    Make a dir and put your raw sequencing data(.fastq files) to the dir.
    Copy the sample config file to your workspace.

  2. Personalize your config file(raw_data, result_dir, refernce_dir, gff, library_type, etc).
  3. Choose the modules you may need(the module list is as above).
  4. Type the command and waiting for the results.

    python ./RNAfinder.py [config_file] [start] [end]

More options and parameters can modified in the config file.

Program Download

The current version of RNAfinder can be downloaded as precompiled binary file.

RNAfinder-1.0.2.Linux_x86_64.tar.gz: pre-built Linux x86_64 binary package

Online server also available on GALAXY

More information can see GitHub and Lulab Wiki


RNAfinder was developed primarily by Wu Yang in Perl. The python version was developed mainly by Luo Haofei and Zhang Shuyang, with significant contributions and suggestions by Di Chao, Yang Yucheng, Yuan Jiapei, Yang Yang, Li Yang, Shi Binbin, and many others. Initial supervision for the project was provided by Professors Zhi John Lu and Wu Yang.

Warning: RNAfinder's source code and pipeline are protected.

You can contact us about RNAfinder at sy-zhang11@mails.tsinghua.edu.cn