WBConfCall 2020.12.17-Agenda and Minutes

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Help Desk



  • CeNGEN
    • Will talk in January for integration into WormBase: who should be on that call?
      • Eduardo, Raymond, Todd, Chris
    • Eduardo has several ideas about how to integrate and display
      • Has slides (for Alliance) with a breakdown of technology over time, species represented (mostly human and mouse)
      • First C. elegans dataset in 2017; another in 2019 with re-annotation of 2017 dataset
      • scRNA-seq data sets are in a big sparse matrix
      • Data in raw FASTQ file --> read alignments --> unfiltered matrix --> barcode filtering --> filtered matrix
      • Data deposited usually at SRA and ENA, but often not raw data, usually the already filtered matrix (sometimes even more processed than that)
      • Human Cell Atlas Data Portal (data.humacellatlas.org) (only human and mouse; not interested in other species)
      • COVID19 cell atlas (covid19cellatlas.org)
      • CellXGene (https://cellxgene.cziscience.com/)
      • Should be analyzing differential gene expression (but not using a t-test)
    • What about the EBI gene expression atlas (gxa): https://www.ebi.ac.uk/gxa/sc/home
      • FlyBase already collaborating with
      • Maybe we can use the tools/infrastructure that EBI GXA has; we could curate into their platform and we can build off of what the GXA has
      • http://europepmc.org/article/MED/31665515
  • Alliance documentation of WormBase data types to pull in
    • Todd has built a document based on Doug Howe's file
    • Todd will share his file
    • Kevin H: if we are pulling everything (of current importance) over to the Alliance in 2 years, we'll need to incorporate pipelines that run during or after our build pipelines
    • We can start with Todd's document and build off of that (keeping a centrally located file)