gtf-compare.md

Method One using our program GTF-Compare

Create virtual evironment with conda

conda create -n ngs-gtf python=3.6 anaconda
source activate ngs-gtf
conda install -c conda-forge pypy3.5
wget https://bootstrap.pypa.io/get-pip.py
pypy3 get-pip.py

Install prerequisites

pypy3 -m pip install gffutils numpy tqdm 'intervaltree<3.0'

Download required files

mkdir -p ~/workdir/gtf-compare/gtfs && cd ~/workdir/gtf-compare/gtfs
ln -s ~/workdir/hisat_align/ref_free.gtf .
ln -s ~/workdir/hisat_align/ref_sup.gtf .
mkdir -p ~/workdir/gtf-compare/method_one && cd ~/workdir/gtf-compare/method_one
wget https://raw.githubusercontent.com/abdelrahmanMA/gtf-compare/master/code/comp.py
wget https://raw.githubusercontent.com/abdelrahmanMA/gtf-compare/master/code/stat.py

Run

source activate ngs-gtf
cd ~/workdir/gtf-compare/method_one
pypy3 comp.py -r ../gtfs/ref_sup.gtf ../gtfs/ref_free.gtf
pypy3 stat.py

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Method Two using GFFCompare

Install gffcompare

source activate ngs-gtf
conda install gffcompare

Run

mkdir -p ~/workdir/gtf-compare/method_two && cd ~/workdir/gtf-compare/method_two
gffcompare -r ../gtfs/ref_sup.gtf ../gtfs/ref_free.gtf