ATAC-seq - Genome Browser (signal + peaks)

[NishiPhalke]

query to fetch ATAC metadata

query fetchATACMetadata {
  atac_metadata {
    sample_id
    sex
    site    
    status
    biospecimen
    entity_id
    opc_id
    protocol
  }
}

query which returns ATAC-seq files. We want to visualize signal and peak files in genome browser.

query FetchDownloadFiles($ome: OmeEnum!) {
  fetch_download_files(ome: $ome) {
    filename
    file_type
    size
    file_ome
    sample_id
    open_access
  }
}

example variables

{
  "ome": "ATAC_SEQ"   
}

All ATAC open access files are hosted at https://downloads.mohdconsortium.org/2_ATAC/[dataset]/[filename] for. e.g https://downloads.mohdconsortium.org/2_ATACMOHD_EA100001/MOHD_EA100001_signal-FC_GRCh38_v0.bigWig

Query returns .bed.gz Peak files. I will generate .bigBed files with same filename as bed.gz only extension will change to .bigBed