| This directory holds functions for downloading raw data needed to train the binding site predictor (classifier) on processed ChIP-seq peaks. |
|
|
| ## Human genome |
| `genome.py` |
| * Download the sequences of all chromosomes from a certain genome (e.g. hg38, used for this project) |
| * Configurations associated with this download can be found in `./configs/data_task/download/genome.yaml` |
|
|
| ### Running the download |
| To run this download, please change directory to `DPACMAN/dpacman` and run: |
|
|
| ``` |
| python -u -m scripts.preprocess data_task=download/genome |
| ``` |
|
|
| ## ReMap 2022 |
| `remap.py` |
| * Download non-redundant peaks: `remap2022_nr_macs2_hg38_v1_0.bed` |
| * Download cis-regulatory modules (CRMS): `remap2022_crm_macs2_hg38_v1_0.bed` |
| * Configurations associated with this download can be found in `./configs/data_task/download/remap.yaml` |
|
|
| ### Running the download |
| To run this download, please change directory to `DPACMAN/dpacman` and run: |
|
|
| ``` |
| python -u -m scripts.preprocess data_task=download/remap |
| ``` |
