Identifying active enhancers and well known transcription factor binding sites from GRO-seq data.
Docker Image to analyze GRO-seq data.
- R 3.0.2
- Python 2.7.2
- Perl v5.18.2
- fastqc 0.10.1
- cutadapt 1.2.1
- BWA 0.7.12
- samtools 0.1.19
- bedtools 2.17.0
- groHMM
- SRA Tools 2.5.4
At first you need to install docker. Please follow the instruction on https://docs.docker.com/installation/
After the successful installation, please follow the online tutorial if you haven't used DOCKER before: https://training.docker.com/introduction-to-docker.
A step-by-step tutorial is available at Tutorial
Data for the tutorial is downloaded from GSE43835.
This experiment looks at GRO-seq data from MCF-7 human breast cancer cells in response to short time course of E2 treatment (10min, 40min) and no treatment (Veh).