Per-sample configuration is stored in samples.tsv, where each row is a single sample. Here, a sample is defined as a single biological replicate in a scATAC datset. The pipeline will pull all necessary data files from the ENCODE portal.
Experiment is the ENCODE accession ID of the sample's dataset.
Replicate is the biological replicate number of the sample on the ENCODE portal.
Modality specifies the experimental protocol used to generate the sample's raw data. Currently supported modalities are:
- 10x single-cell ATAC (10x)
- 10x Single Cell Multiome ATAC + Gene Expression (multiome)
- Bing Ren lab split-pool scATAC (ren)
Genome specifies the target genome for alignment and analysis. The pipeline currently supports GRCh38 (human) and mm10 (mouse).
Note: Lines starting with # will be ignored.
Global configuration parameters are stored in config.yaml. (Visit here for a YAML cheat sheet.)
🚧 Under construction 🚧