Délara Sabéran-Djoneidi, Anne-Laure Schang, Kate Wooley-Allen, Sascha Ott
Alix Silvert, Magali Hennion
This repository has been made to be used as a starting base for your own ATAC-Seq analysis.
The file ATACseq.ipynb presents analyses allowing you to go from raw fastq files up to called ATAC-Seq peaks. This is a jupyter notebook prepared with a small example which your personnal machine should be able to run. ATACseq-all4samples_v3.ipynb is a similar notebook, but allowing to process several samples at once.
Similarly, the file differential_binding.ipynb presents a comparison study between several ATAC-Seq samples, run with edgeR in R. This is also a jupyter notebook which uses the files generated by the small example in the previous Jupyter Notebook.
Please adapt it for your personnal uses.