README.md

#Introduction

This project aim is to provide simple tool that creates BigBed file from gene definition downloadable from UCSC. The script is designed to be run on linux and uses heavily tools provided by UCSC: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

#Usage

Download definition of genes. For instance to download refGene definition for human hg38 reference genome execute:

curl http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz -o refGene.txt.gz

Now you can call the script providing as an input file with genes and identifier of the reference genome:

python3 generate.py refGene-19.txt.gz hg19

This should generate file called refGene.bb