Identifying active enhancers and well known transcription factor binding sites from GRO-seq data.
This a fork of Kraus-Lab/active-enhancers, rewritten to use Nextflow to streamline the use.
nextflow run Functional-Genomics-Lab/active-enhancers -profile utd_ganymedeResults of the reproduction can be viewed on Hugging Face
These are all built and installed via Wave containers
- 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
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 (Vehicle).