Data curation

[khoroshevskyi]

Data that needs to be uploaded to bedbase:

• LOLA
  • hg19
    • https://pephub.databio.org/databio/lola_hg19_cistrome_epigenome?tag=default
  • hg38
    • cistrome_cistrome [ https://pephub.databio.org/databio/lola_hg38_cistrome_cistrome?tag=default ]
    • cistrome_epigenome [https://pephub.databio.org/databio/lola_hg38_cistrome_epigenome?tag=default]
    • codex (not hg38)
    • encode_segmentation [ https://pephub.databio.org/databio/lola_hg38_encode_segmentation?tag=default ]
    • encode_tfbs
    • sheffield_dnase
    • 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

[khoroshevskyi]

This issue was partially finished, and is not high priority anymore.
All LOLA, Encode for hg38 was uploaded to bedbase.
GEO is automatically uploading to BedBase

[khoroshevskyi]

Other resources to conciser:

• http://remap.univ-amu.fr
• http://cistrome.org/db