icSHAPE-pipe

icSHAPE-pipe is a pipeline to calculate icSHAPE score in genome with sliding window strategy.

Installation

Prerequisites

Python ≥ 2.7

Python packages:

• pysam: https://pypi.org/project/pysam/
• numpy: http://www.numpy.org
• pandas: https://pypi.org/project/pandas/
• matplotlib: https://pypi.org/project/matplotlib/
• seaborn: https://seaborn.pydata.org
• sklearn: https://scikit-learn.org/stable/

Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

STAR: https://github.com/alexdobin/STAR > 2.5.0

hisat2: https://ccb.jhu.edu/software/hisat2/index.shtml (optional)

Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic Embedded

cufflinks: http://cole-trapnell-lab.github.io/cufflinks/

samtools: http://www.htslib.org/download/

GNU GCC > 4.7 (not required for Linux)

libhts: http://www.htslib.org (not required for Linux)

Installing

1. Add these lines to your ~/.bash_profile, [icSHAPE-pipe] is the absolute path of icSHAPE-pipe.

   export PATH=[icSHAPE-pipe/bin]:$PATH

2. If your operation system is Linux, skip this step. The executable files have been static compiled.

   1. Compile PsBL library

      cd [icSHAPE-pipe]/PsBL
      make && make install

   2. Configure your environment. Add these lines to your ~/.bash_profile

      LIBPATH=[icSHAPE-pipe]/PsBL/PsBL
      CPLUS_INCLUDE_PATH=$LIBPATH/include:$CPLUS_INCLUDE_PATH
      LIBRARY_PATH=$LIBPATH/lib:$LIBRARY_PATH
      LD_LIBRARY_PATH=$LIBPATH/lib:$LD_LIBRARY_PATH
      DYLD_LIBRARY_PATH=$LIBPATH/lib:$DYLD_LIBRARY_PATH

   3. Compile icSHAPE-pipe

      cd [icSHAPE-pipe]
      make && make install

3. Make sure these files are excutable

   chmod +x [icSHAPE-pipe]/GAP/parseBedFromGTF.py
   chmod +x [icSHAPE-pipe]/bin/Functions/sam2tab
   chmod +x [icSHAPE-pipe]/bin/Functions/calc_sliding_shape
   chmod +x [icSHAPE-pipe]/bin/Functions/countRT

Framework

More usage information

ZhangLab

Example

Example data

Authors

• Li Pan - Programmer - Zhanglab