ATAC-CNV

Prepare data

Download data from this Nature Biotech paper and put into data/

Configure Environment

1. Download R
2. Install CopyscAT as directed in the tutorial.

Rstudio is one of the most widely used IDE. The community version is open source. Jupyter also provides R kernel, but I do not have personal expeirence with it.

Use CopyscAT to process data

1. Run prep-genome.R. You may need to install BSgenome.Hsapiens.UCSC.hg19

2. Run process_fragment_file.cmd. You will need Python.

3. Run obtain-cnv.R.

Prepare genome

Run prep-genome.R. You may need to install BSgenome.Hsapiens.UCSC.hg19

Find CNV

Run obatin-cnv.R

Downstream analysis

Run MPAL1.ipynb