/protein-fusion-pipeline

Pipeline to detect protein fusions using Arriba

Primary LanguageShell

protein-fusion-pipeline

Requirements:

- samtools
- arriba

Create a conda environment with the required packages:

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

conda create --n arriba
conda activate arriba

conda install -c bioconda arriba
conda install -c bioconda samtools

Run the pipeline

qsub ExtractSamples.sh batchid

list=$(cat samples_batchid.txt )

for l in $list; do echo ${l}; qsub Alignment.sh ${l} batchid; done

for l in $list; do echo ${l}; qsub ProteinCalling.sh ${l} batchid; done

for l in $list; do echo ${l}; qsub CheckAlignReads.sh ${l} batchid; done

NOTE:https://arriba.readthedocs.io/en/latest/quickstart/