ADAMA web-service wrapper to transform "Chromatin States" GFF3 data into JBrowse compatible JSON
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README.md

Chromatin States to JBrowse web services

Objective: Build a simple web service which parses standalone GFF3 files containing high-resolution maps of chromatin states based on DNA and epigenetic data, and returns this data in JBrowse compatible JSON format.

The adapter utilizes gffutils to process the input GFF3 file, creating an intermediary sqlite database for fast data retrieval.

Reference:
Joana Sequeira-Mendes, Irene Aragüez, Ramón Peiró, Raul Mendez-Giraldez, Xiaoyu Zhang, Steven E. Jacobsen, Ugo Bastolla, and Crisanto Gutierrez (2014) The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. Plant Cell, doi:10.1105/tpc.114.124578

Requirements:

  • Enable the following plugin in JBrowse within tracks.conf:
[plugins]
Araport.location = ./plugins/Araport
  • This adapter relies on storing the GFF3 file(s) correspoding to the 9 chromatin states within the repository in the data/ sub-directory.
data/tpc124578_SupplementalDS2-state_1.gff3
data/tpc124578_SupplementalDS2-state_2.gff3
data/tpc124578_SupplementalDS2-state_3.gff3
data/tpc124578_SupplementalDS2-state_4.gff3
data/tpc124578_SupplementalDS2-state_5.gff3
data/tpc124578_SupplementalDS2-state_6.gff3
data/tpc124578_SupplementalDS2-state_7.gff3
data/tpc124578_SupplementalDS2-state_8.gff3
data/tpc124578_SupplementalDS2-state_9.gff3
  • Ensure that the chromatin_states_to_jbrowse adapter is registered and accessible via ADAMA. See metadata.yml for adapter configuration (list of dependency modules and REST endpoints described using swagger.io spec).

  • Set up the following track configuration in JBrowse within trackList.json:

{
    "style": {
        "color": "red"
    },
    "key": "Chromatin State 1",
    "storeClass": "Araport/Store/SeqFeature/REST",
    "baseUrl": "https://api.araport.org/community/v0.3/vivek-dev/chromatin_states_to_jbrowse_v0.1",
    "compress": 0,
    "type": "JBrowse/View/Track/CanvasFeatures",
    "category": "Motifs / Chromatin States (Sequeira-Mendes et al. 2014)"
    "metadata": {
        "Description": "High-resolution map of chromatin state 1, characterized by high amounts of H3K4me2 and H3K4me3, H3 acetylation, H3K36me3, and H2Bub, typically associated with transcribed regions",
        "Source": "Sequeira-Mendes, et al. 2014 (Plant Cell)",
        "URL": "http://www.plantcell.org/content/early/2014/06/11/tpc.114.124578"
    },
    "glyph": "JBrowse/View/FeatureGlyph/Box",
    "label": "chromatin_state_1",
    "query": {
        "chromatin_state": 1
    }
}

Repeat the above configuration stanza for the rest of the chromatin states (2-9), altering the following key-value pairs in the config:

  • key
  • label
  • query -> chromatin_state.
  • metadata -> Description
  • style -> color

Demo:

Above screenshot shows the color-coded chromatin domain annotations over an ~50-kb region of the Arabidopsis Chromosome 1 (Chr1:11350001..11410863) being rendered in JBrowse