Data curation

[khoroshevskyi]

Data that needs to be uploaded to bedbase:

• [ ] LOLA
  • [ ] hg19
  • [x] https://pephub.databio.org/databio/lola_hg19_cistrome_epigenome?tag=default
  • [ ] hg38
  • [x] cistrome_cistrome [ https://pephub.databio.org/databio/lola_hg38_cistrome_cistrome?tag=default ]
  • [x] cistrome_epigenome [https://pephub.databio.org/databio/lola_hg38_cistrome_epigenome?tag=default]
  • [x] codex (not hg38)
  • [x] encode_segmentation [ https://pephub.databio.org/databio/lola_hg38_encode_segmentation?tag=default ]
  • [x] encode_tfbs
  • [ ] sheffield_dnase
  • [x] ucsc_features [ https://pephub.databio.org/databio/lola_hg38_ucsc_features?tag=default ] Faild: 'coriellDelDup', 'rmsk', 'switchDbTss'
  • [ ] mm10
  • [ ] mm9
  • [ ] rn6
• [ ] ENCODE
• [ ] GEO
• [ ] http://catlas.org/catlas_hub/
• [ ] other data?

[khoroshevskyi]

LOLA structure: . ├── hg19 │ ├── cistrome_cistrome │ ├── cistrome_epigenome │ ├── codex │ ├── encode_segmentation │ ├── encode_tfbs │ ├── sheffield_dnase │ └── ucsc_features ├── hg38 │ ├── cistrome_cistrome │ ├── cistrome_epigenome │ ├── codex │ ├── encode_segmentation │ ├── encode_tfbs │ ├── sheffield_dnase │ └── ucsc_features ├── mm10 │ ├── codex │ ├── encodeTFBSmm10 │ └── ucsc_features ├── mm9 │ ├── codex │ ├── encodeTFBSmm9 │ └── ucsc_features ├── rn6 │ ├── codex │ ├── encodeTFBSrn6 │ └── ucsc_features └── test ├── cistrome_cistrome └── encode_tfbs

[khoroshevskyi]

ENCODE: https://github.com/databio/bedbase_encode

[donaldcampbelljr]

An update: On Tuesday we uploaded: lola_hg19_cistrome_epigenome. not hg38 https://pephub.databio.org/databio/lola_hg19_cistrome_epigenome?tag=default