==== Omics Data Standards WG - Minutes 01-09-2017 ====

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Document for ChIA-PET standards

Protocol

  * Relation to current technologies such as Hi-ChIP and PLAC-seq
      * ChIA-PET is a more mature stand-alone method that deserves its position in the documentation
      * Do we need to compare ChIA-PET and other protocols, mentioning those so that people can expect what their data may look like
      * Standard can be defined in a way to allow future improvements to the protocol, together with a basic standard for the technology
  * Library quality controls
      * At the end of the documents, QC for various steps of library are listed
      * Basic numbers, key steps for QC
        * Number of cells: 1e8 (100M) would be comfortable, less is doable but may result in complexity problems and may be affected by PCR redundancies
        * Antibody robustness: follow the current parameter from ENCODE regarding to ChIP-seq, antibodies able to generate qualified ChIP-seq data should be good enough for ChIA-PET
        * Sequencing can be done in two levels: 1) sequencing on known binding sites to verify; 2) should pass miSeq QC first, then the number of reads should be ~100M to ~150M
  * Proximity ligation would affect ChIA-PET library quality (without ligation the results become ChIP-seq). Chromatin contact can be used to verify.
  * Collision rate to assess QC
  * Gold standard loops or features for ChIA-PET
      * For example, MALAT1-NEAT1 interaction in Hi-C

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