# Changelog

## 113
### File layout changes
The `Peaks` folder for human and mouse has been restructured to be consistent with other species and to avoid data duplication. Peaks are now available as bigBed files in the `peaks` folder, which is further organised by assay type. Signal files (as bigWig) are now also available in the `signal` folder.

The `MotifFeatures` directory has been removed. Motif features are now available in the annotation folder.

The regulatory features gff file in the top-level folder (`homo_sapiens`) will be removed in release 114.

### ID changes
Annotation uses a new ID system. Features can be mapped between releases using `feature_mapping_113_to_112.tsv.gz` in `GRCh38/annotation`.

## 112
### File layout changes
GRCh38 files will progressively be moved to the `GRCh38` folder over the next few releases (112-114).

- Regulatory features (gff) are now available in `GRCh38/annotation`, with the following naming convention: `<species>.<assembly>.regulatory_features.v<release>.gff3.gz`. This annotation file also contains links between promoters and their associated gene(s). The gff file in the top-level folder (`homo_sapiens`) will be removed in release 114.
- Regulatory feature activity is no longer available as one gff file per cell type. Instead, activity is available as a tsv file in the `GRCh38/annotation` folder. The tsv file contains activity across all cell types for all features. 

### Promoter annotation
Promoters now align to the 5'-ends of transcripts from GENCODE Comprehensive. More specifically, they align 10 bp downstream of a putative Transcript Start Site (TSS). This means that some regulatory features have been split and some have been combined. The mapping between v111 and v112 features is available in the file `feature_mapping_112_to_111.tsv.gz` in `GRCh38/annotation`.