Question: What annotations are included in the downloadable reference genomes for Cell Ranger ATAC?
Answer: The following annotations are included in the reference genomes for Cell Ranger ATAC:
- Ensembl annotated promoter and enhancer regions.
- ENCODE annotated DNase hypersensitivity regions.
- GENCODE annotated TSS (Transcription Start Site) for each transcript.
- Transcription factor motifs from JASPAR (http://jaspar.genereg.net/) vertebrate non-redundant collection.