Usage

EpitopeID identifies and determines the genomic location of epitopes or other inserted sequences relative to genomic loci.

Figure1A

bash identify-Epitope.sh -i /path/to/FASTQ -o /path/to/output -d /path/to/genome/database [-t <Threads - Default 1>] [-p <Pvalue - Default 0.05>]
eg: bash identify-Epitope.sh -i /input -o /output -d /sacCer3_EpiID -t 2 -p 0.1

Dependencies

The following dependencies are needed to run EptiopeID.

Bedtools v2.26+
Bowtie v2.2.5+
GNU grep
Perl5
Python v3.7+
- Scipy
Samtools v1.7+
wget

Anaconda
Singularity

You can install these dependencies as a conda environment if you have conda setup on your machine using the following command:

conda create -n epitopeid-env -c bioconda -c conda-forge bedtools bowtie2 perl scipy pysam wget grep samtools

...and then turn on the environment with:

conda activate epitopeid-env

Dependencies​

Dependencies