==== Omics Data Standards WG - Minutes 11-14-2016 ====

|~~TABLE_CELL_WRAP_START~~<WRAP>

  - Standard guidelines. Consist of experimental part and protocols, agreed on using the in situ Hi-C paper as a standard. Minor variations on the experimental protocols. This document may be updated on an annual basis and will be kept stable in the meantime. Concerns:
      - Which other enzymes can be used? Hind III give very good quality data
      - and are more reproducible but may have lower resolution than 4-base cutters. The current wording allows individual PIs to choose their restriction enzyme based on their current situation.
      - Biotin removal step will affect yield and should be kept optional instead of mandatory. The SOP will be without biotin removal (all published in situ Hi-C data have no such step).
      - All variations from the base protocol (SOP) should be recorded in the meta data so that DCIC can work on those.
      - Cell density at the time of harvest: Is the cell density need to be standardized? \__Suspension cells will be in per unit volume and adherent cells will be in per unit area.
        - Although this appears out of scope - it need to be included in experimental / cell-line WG SOP so that researchers will record it before actually generating data (and submitting them), it might still be OK to include in this data standard document.
      - Indicating whether there are other frozen aliquots and point to them in meta data so that people know which datasets are coming from the same biological replicate.
      - Crosslinking: standardized in SOP and have no dramatic differences among groups.
      - Sequencing Depth: required 500M raw paired-end sequence reads now in the final document.
      - Earlier experiments may use variations.
  - Format for pairs file. Standardized file format for read pairs (developed by Burak), text-based file before chromosomal binning. Planned to be approved during next meeting: .
  - ChIA-PET. Defer to the next meeting
  - Other data types
  - Joint WG of OMICS and Images. Maybe incorporate a larger group than the current OMICS WG to include some members from the imaging WG.

\\ \__
</WRAP>~~TABLE_CELL_WRAP_STOP~~|