Pipeline for mapping and counting TGIRT RNA-seq
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 [email protected]: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 .
cd scripts
snakemake -s make_ref.smk -p -j2
It is necessary to install sequencing_tools to run the pipeline correctly as the pipeline extensively used some of the tools.