TGIRT-map

Pipeline for mapping and counting TGIRT RNA-seq

Start

Installation

Using conda to create an environment

conda config --add channels r
conda config --add channels bioconda

conda create -q -n tgirt_map python=3.6 \  
        pandas biopython cython numpy networkx seaborn pyBigwig six pysam ujson \
        hisat2 bowtie2=2.2.5 bedtools samtools snakemake bedtools atropos seqkit \
        xopen ucsc-gtftogenepred ucsc-genePredToBed bedops xopen 
source activate tgirt_map

Download TGIRT-map

git clone git@github.com:wckdouglas/tgirt_map.git
cd tgirt_map
pip install .

# install sequencing tools
cd ../
git clone https://github.com/wckdouglas/sequencing_tools.git
cd sequencing_tools
pip install .

prepare references

cd scripts
snakemake -s make_ref.smk -p -j2 

Required pacakge

It is necessary to install sequencing_tools to run the pipeline correctly as the pipeline extensively used some of the tools.