8  Install CIRIquant and CIRCexplorer3

8.1 CIRIquant

  • Complete documentation can be found in CIRIquant.

  • My purpose is to show some of the basic scripts to run CIRIquant repeatedly.

  • Create an environment quant to install all dependencies and packages.

Warning

ciriquant 1.1.2 has requirement pysam==0.15.2 ciriquant 1.1.2 has requirement PyYAML==5.1.1 ciriquant 1.1.2 has requirement python==2.7

conda create -n quant python=2.7 PyYAML=5.1.1 pysam=0.15.2
conda activate quant
conda install -c bioconda bwa
conda install -c bioconda hisat2
conda install -c bioconda stringtie
pip install ciriquant

  • Make sure all the following tools are installed i.e., bwa, hisat2, samtools, stringtie

  • And finally check

CIRIquant -h

8.2 CIRCexplorer3

  • Create a Python 2 environment named py2, install Python 2.7

  • Install circexplorer2 and required softwares (python version 2.7.1 encouraged)

conda create --name py2 python=2.7
conda activate py2
conda install circexplorer2 --channel bioconda
conda install -c bioconda bowtie==1.0.0 
conda install -c bioconda samtools==0.1.18
conda install -c bioconda hisat2
conda install -c bioconda stringtie
conda install -c bioconda tophat==2.1.0
  • Install CLEAR_QUANT
wget https://github.com/YangLab/CLEAR/archive/refs/heads/master.zip
cd CLEAR-master/
python setup.py install