====== Omics Data Standards ====== **The mailing list for the working group has been changed. Please use [[omics@4dnucleome.org|]] from now on as the new mailing list address.** ===== Introduction ===== The Omics Data Standard Working Group will establish common standards, quality metrics, and data formats for the Omics experiments, datasets, and feature annotations to be produced and released by the 4DN consortium. ===== Mission / Objectives ===== The Omics Data Standard Working Group will establish common standards, quality metrics, and data formats for the Omics experiments, datasets, and feature annotations to be produced and released by the 4DN consortium. ===== Omics Standards Discussion Group ===== [[https://groups.google.com/a/4dnucleome.org/forum/#!forum/omics-standards|The Omics Standards Discussion Group]] (click link to follow) has been created to enable discussions on detailed experimental parameters (for example, ChIP-Seq antibodies) for all technologies involved within the network. All 4DN members are encouraged to apply if their work involves any of the related technologies. If you wish to receive email updates for everything happening in this group, please use the button "**Apply to join group**" above, set your email preferences in "**Email delivery preference**" in the popped up panel, **tell us who you are (name and affiliation)** and, if you are not a 4DN PI, which 4DN PI you are associated with, then click **Apply to join this group.** ===== Meetings ===== Omics conference meetings are held twice a month via WebEx, on the 2nd and 4th Monday of each month at 11am PST/1pm CST/2pmEST. Each call lasts approximately 1 hour. WebEx conference calls information is below. __Please use the following link to incorporate edits and protocol changes ahead of time:__ [[https://docs.google.com/document/d/1BBHkwrilTaL6N8dQ-QJE5KXKRrZaox3hD7XdEoVyII8/edit|https://docs.google.com/document/d/1BBHkwrilTaL6N8dQ-QJE5KXKRrZaox3hD7XdEoVyII8/edit]] |~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__Second Monday__ ** The 2nd Monday of every month from Monday, March 14, 2016, to Monday December 11, 201 11:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m75db95e39193f63aae5023f31de4c2b9&sa=D&sntz=1&usg=AFQjCNGr15bi-nq1A2MUSwON9moJJaOimQ|Join WebEx meeting]] Meeting number: 805 470 441 Meeting password: KME4Q7Ew **Join by phone** +1-415-655-0002 US Toll Access code: 805 470 441 ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__Fourth Monday__ ** The 4th Monday of every month from Monday, May 23, 2016 , to no end date 11:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m7ad3cf889e062e15c746d05cdd02ec9c&sa=D&sntz=1&usg=AFQjCNHtPpBDetR_6SDgw2ruW-yHY5j_ZQ|Join WebEx meeting]] Meeting number: 807 058 449 Meeting password: pJhzCW2m **Join by phone** +1-415-655-0002 US Toll Access code: 807 058 449 ~~TABLE_CELL_WRAP_STOP~~| The **Allele Specific Omics Data Standards Group** will meet 2nd and 4th Wednesdays of the month at 10AM PT (1PM EST). The first call will be on Nov 22, 2017. |~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__Second Wednesday__ ** The 2nd Wednesday of every month from Wednesday, December 13, 2017, to no end date 10:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr **__[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m75db95e39193f63aae5023f31de4c2b9&sa=D&sntz=1&usg=AFQjCNGr15bi-nq1A2MUSwON9moJJaOimQ|Join WebEx meeting]]__ ** Meeting number: 804 302 182 Meeting password: PTPvVvF8 **Join by phone** __+1-415-655-0002__ US Toll Access code: 804 302 182 ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__Fourth Wednesday__ ** The 4th Wednesday of every month from Wednesayday, November 22, 2017, to no end date 10:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr **__[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m7ad3cf889e062e15c746d05cdd02ec9c&sa=D&sntz=1&usg=AFQjCNHtPpBDetR_6SDgw2ruW-yHY5j_ZQ|Join WebEx meeting]]__ ** Meeting number: 806 649 089 Meeting password: 9rkJs4Mb **Join by phone** __+1-415-655-0002__ US Toll Access code: 806 649 089 ~~TABLE_CELL_WRAP_STOP~~| The **Single Cell Standards Group** will meet 1st and 3rd Wednesdays of the month at 9AM PT (12PM EST). The first call will be on Nov 15. |~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__First Wednesday__ ** The 1st Wednesday of every month from Wednesday, December 6, 2017, to no end date 9:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr **__[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m75db95e39193f63aae5023f31de4c2b9&sa=D&sntz=1&usg=AFQjCNGr15bi-nq1A2MUSwON9moJJaOimQ|Join WebEx meeting]]__ ** Meeting number: 801 959 044 Meeting password: UvGRxga4 **Join by phone** __+1-415-655-0002__ US Toll Access code: 801 959 044 ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ **WebEx info Call-__ Third Wednesday__ ** The 3rd Wednesday of every month from Wednesday, November 15, 2017 , to no end date 9:00 am| Pacific Daylight Time (San Francisco, GMT-07:00| 1hr **__[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m7ad3cf889e062e15c746d05cdd02ec9c&sa=D&sntz=1&usg=AFQjCNHtPpBDetR_6SDgw2ruW-yHY5j_ZQ|Join WebEx meeting]]__ ** Meeting number: 805 001 599 Meeting password: Ustw3jZi **Join by phone** __+1-415-655-0002__ US Toll Access code: 805 001 599 ~~TABLE_CELL_WRAP_STOP~~| **WEBEX CONTACT INFORMATION:** Catherine Rivera-Noel [[oh@4dnucleome.org|]] ===== Documents ===== ^**Meeting~~CKG_TABLE_NBSP~~Date** ^**Agenda** ^**Minutes** | |~~TABLE_CELL_WRAP_START~~ 12-11-2015 ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ * Discussion of mission ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/document/d/1wPQygR1at6ureVlO2Jp8J629l6WyWmIiWmUEs4aKi0s/edit?usp=sharing|minutes prepared by bing ren]] ~~TABLE_CELL_WRAP_STOP~~| |2-8-2016|~~TABLE_CELL_WRAP_START~~ * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=0c97564b7581589e46fd4fcc9bc57cc1&sa=D&sntz=1&usg=AFQjCNE1zkar32Xt55CaNaJincta9f_n8A|Presentation by Erez]] * [[https://docs.google.com/document/d/1GeZdeFNfGt6fH7RiuRyhZ4eSt3RBAGPvDuG1ONfAE0o/edit?usp=sharing|Discussion of HiC standard]] * [[https://docs.google.com/document/d/1Pn_sG0Jv6RRXE0dmSkbF_cKvSBESlpXQNAuKM4dcgFM/edit?usp=sharing|Publication Policy WKG questions]] ~~TABLE_CELL_WRAP_STOP~~|Erez gave a presentation focused on the analysis pipeline of in situ HiC data. The software includes: mapping, normalization, reproducibility analysis, domain calls, loop calls, and visualization. The package is publicly available at GitHub.| |2-22-2016|~~TABLE_CELL_WRAP_START~~ * [[https://docs.google.com/document/d/1GeZdeFNfGt6fH7RiuRyhZ4eSt3RBAGPvDuG1ONfAE0o/edit?usp=sharing|Discussion of HiC standard]] * [[https://docs.google.com/document/d/1Pn_sG0Jv6RRXE0dmSkbF_cKvSBESlpXQNAuKM4dcgFM/edit?usp=sharing|Publication Policy WKG questions]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-for-2-22|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |3-14-2016|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| |3-28-2016|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~| |5-23-2016|~~TABLE_CELL_WRAP_START~~ * Discussion of data file format specifics ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-05-23-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |6-13-2016|~~TABLE_CELL_WRAP_START~~ * Discussion of experiment protocols * Discussion of standard data formats ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016|Meeting minutes]]\\ Google docs links for [[https://docs.google.com/document/d/1BBHkwrilTaL6N8dQ-QJE5KXKRrZaox3hD7XdEoVyII8/edit?usp=sharing|experiment protocols]] and [[https://docs.google.com/document/d/1WmLyQ7PFQlBn2z4vDMKkmOAxFEZw9dJou7-AjoKHNVs/edit|data formats]], for suggestions and comments ~~TABLE_CELL_WRAP_STOP~~| |6-27-2016|~~TABLE_CELL_WRAP_START~~ * Determine experimental protocols * Discussion of meta-data * Discussion of data formats ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-27-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |7-11-2016|~~TABLE_CELL_WRAP_START~~ * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NWJmNTBkMjQzMTYwYWVhNQ|DCIC plans and metadata overview]] * [[https://docs.google.com/document/d/15tuYHENH_xOvtlvToFJZMzm5BgYFjjKJ0-vSP7ODOG0/edit|HiC (and more) metadata draft]] * [[http://www.google.com/url?q=http://www.cell.com/cms/attachment/2078691992/2071115658/mmc2.xlsx&sa=D&sntz=1&usg=AFQjCNFWXlGvTHEaDK92j3WGD_vZLAC62Q|.hic format]]; [[https://docs.google.com/a/broadinstitute.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0YTRmZjgzYWIxN2E2NTU0|slides]] * [[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NWIxNmQzMDEyNjE3YzQ5Yg|BUTLR and 3D Genome Browser]] * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NDNjMjg1NmQxMDAwMDEwMA|Format Considerations, HDF5, Cooler]] * Nezar Abdennur - Mirny Lab ~~TABLE_CELL_WRAP_STOP~~|~~CKG_TABLE_NBSP~~| |7-25-2016|~~TABLE_CELL_WRAP_START~~ * Discuss about file formats ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-25-2016|Meeting minutes ]] ~~TABLE_CELL_WRAP_STOP~~| |8-8-2016|~~TABLE_CELL_WRAP_START~~ * Discuss about file formats and benchmark methods / results ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-08-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |8-22-2016|~~TABLE_CELL_WRAP_START~~ * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MzI1ZDIyMDcwOTExYWY2YQ|20160822 metadata Andy Schroeder for DCIC.pptx]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-22-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |9-12-2016|~~TABLE_CELL_WRAP_START~~ * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6Mjc0NjQzOWIwYTEyOTI0Ng|Matrix file format usability review report]] * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MWUzMGRkMjEwYmNkMTdlNQ|DCIC proposal for HiC processing pipeline (backbone)]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-09-12-2016|Meeting minutes ]] ~~TABLE_CELL_WRAP_STOP~~| |9-26-2016|~~TABLE_CELL_WRAP_START~~ * OMICS year 1 report * Dataset requirements (coverage, etc.) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-09-26-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |10-24-2016|~~TABLE_CELL_WRAP_START~~ * Hi-C data standards (replicates, sequencing depth) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |11-14-2016|~~TABLE_CELL_WRAP_START~~ * Finalizing data standards for Hi-C * [[https://docs.google.com/document/d/14VSxYZ8NpX47NHx7TE8_koD7J53nTpA_SAuuyNhTANA/edit?usp=sharing|Filtered pairs (contact list) file format specification]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |11-28-2016|~~TABLE_CELL_WRAP_START~~ * ChIA-PET protocols and standards ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-11-28-2016|Meeting minutes]]\\ Presentation ~~TABLE_CELL_WRAP_STOP~~| |12-12-2016|~~TABLE_CELL_WRAP_START~~ * Definition of loops ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-12-12-2016|Meeting minutes]]\\ Presentation from Suhas Rao ~~TABLE_CELL_WRAP_STOP~~| |1-9-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of ChIA-PET data standard and guidelines ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozYTM1N2M2MzI4MDJkMWI|Draft ChIP-PET protocol (from Y Ruan)]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-09-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |2-13-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of ChIA-PET and PLAC-seq ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ Presentation from Rongxin Fang\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-13-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |2-27-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of future OMICS WG plans ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/spreadsheets/d/1eNajg-wroy9Ruj7xAj6i087nm-eM54ueFrBuP5m7JsU/edit?usp=sharing|Spreadsheet for tentative future topics and date]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-27-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |3-13-2017|~~TABLE_CELL_WRAP_START~~ * Discussion about Repli-seq ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3OGQxYjE1YmU1NWUzNWYz|Slides for Repli-seq]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-03-13-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |4-10-2017|~~TABLE_CELL_WRAP_START~~ * Hi-C data submission and processing plans ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MWQ2MjlkMDU4OTAzYjBi|DCIC Metadata Slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-04-10-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |4-24-2017|~~TABLE_CELL_WRAP_START~~ * Alignments of Hi-C * [[https://docs.google.com/a/broadinstitute.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozM2YzNjY3MDcyY2U1Njky|Read mapping]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-04-24-2017|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2MmU5ZmEyNGM2OGY5MDJj|DCIC presentation]] ~~TABLE_CELL_WRAP_STOP~~| |5-8-2017|~~TABLE_CELL_WRAP_START~~ * Hi-C Alignments and Normalization Procedures * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoxMDgxMDQ2ZTliYzRjMzI3|Alignment slides (DCIC)]] * [[https://docs.google.com/a/broadinstitute.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0ZWFkMzk4YjE2NjVmYzQz|Normalization slides (from DAWG meeting)]] ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-05-08-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |5-22-2017|~~TABLE_CELL_WRAP_START~~ * Repli-Seq protocol and standards. ([[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyZjNmNGU4ZGQ4ZmJlZjQw|Protocol]], [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozNWFiMzhjODIzYjdiMTBi|Standards]])\\ OMICS members on call has approved the E/L Repli-seq documents through Step 9 and they will be sent to 4DN SC for final approval. An updated Step 10 will be jointly presented by DCIC and Gilbert Lab and be approved later. * Hi-C Read Alignment * Hi-C Normalization ([[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo5Zjg1ZWZiMTQ2NTYyNGQ|Slides]]) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-05-22-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |6-12-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of HG38 vs. HG19. Which version should be used by 4DN? Pros and cons * Concepts of chromatin loops, domains. Collection of opinions. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-12-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |6-26-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of norm test (Burak/DCIC). * Finishing up discussion of hg19 vs hg38, * Compartment calling ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-26-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |7-10-2017|~~TABLE_CELL_WRAP_START~~ * Discussion of norm test (Burak/DCIC). ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0N2M0MWNkNTlkYjFjM2Qw|DCIC update slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-10-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |7-24-2017|~~TABLE_CELL_WRAP_START~~ * Discussion an updated ChIA-PET protocol and guideline (Yijun Ruan) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ ChIA-PET updated protocol\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoxYWNiZWJlNmQ2MzEyOWUw|ChIA-PET slides]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-24-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |8-14-2017|~~TABLE_CELL_WRAP_START~~ * Continued discussion an updated ChIA-PET protocol and guideline (Yijun Ruan) * A proposed DCIC HI-C processing pipeline (Peter Park) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo1OGQ5MDU4M2UwMjNhZGNh|DCIC slides]]\\ [[https://docs.google.com/document/d/1ti2YJ-gHSBCBq4DL5iMdCFDE_bQP1LCgJFfEYTte0iY/edit#heading=h.uvjjc19carml|DCIC document ]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-14-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |8-28-2017|~~TABLE_CELL_WRAP_START~~ * Continue discussion with Chia-PET data analysis * Continue discussion DCIC proposal regarding Hi-C visualization and process pipeline ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-28-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |10-9-2017|~~TABLE_CELL_WRAP_START~~ * [[https://docs.google.com/document/d/1xaPsuobGvyWc7T7Gq3nZwFnDK2jlGMZ-U94pBDKwAKU/edit?usp=sharing|Summary of action items from the Consortium meeting]] * Identify related techniques that are practiced by multiple groups, and form sub-groups for the drafting of experimental protocols and data standards of these methods. * Identify techniques that are being practiced by single labs, and schedule the discussion protocol/data standards. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-10-09-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |10-23-2017|~~TABLE_CELL_WRAP_START~~ * Discuss about the strategies for single cell Hi-C and allelic analysis data sets. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-10-23-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |11-13-2017|~~TABLE_CELL_WRAP_START~~ * DNase-HiC protocol (Vijay Ramani from Jay Shendure lab) * Discussion * Single cell combinatorial indexing Hi-C protocol (sciHi-C) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-11-13-2017|Meeting minutes]]\\ Slides ~~TABLE_CELL_WRAP_STOP~~| |11-27-2017|~~TABLE_CELL_WRAP_START~~ * Update on PLAC sub working group discussion (Miao Yu) * Update on single cell Hi-C (Burak Alver) * Update on allelic analysis of Omics data (Burak Alver or someone) * Feedbacks and discussion of DNase-HiC and sciHi-C ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-11-27-2017|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |1-8-2018|~~TABLE_CELL_WRAP_START~~ * Update on the sub-working group focusing on PLAC-seq standard (Miao Yu) * Update on the sub-working group focusing on single cell Hi-C discussion (Burak Alver) * Update on the sub-working group focusing on allelic analysis of HiC and other OMICS data (Burak Alver) * Vote to recommend the approval of the Dnase-HiC protocol ([[https://www.google.com/url?q=https://www.nature.com/articles/nprot.2016.126&sa=D&sntz=1&usg=AFQjCNE5HU4gloTdeNRy_VV-aHud3Ey6iA|link here]]). This protocol was presented by Vijay Ramani from Jay Shendure lab on November 13. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-08-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |1-22-2018|~~TABLE_CELL_WRAP_START~~ * Update from sub-working group on PLAC-seq/HiChIP (Miao Yu) * Update from sub-working group on single cell Hi-C (Burak Alver) * Presentation of SPRITE (Sofia Quinodoz/Guttman Lab) followed by discussion. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view|SPRITE protocol]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-22-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |2-12-2018|~~TABLE_CELL_WRAP_START~~ * Updates on the sub-working groups. * Potential feedbacks on the SPRITE protocol. * Scheduling of additional OMICS protocols for future discussion. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-12-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |2-26-2018|~~TABLE_CELL_WRAP_START~~ * Updates on the sub working groups ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-26-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |3-12-2018|~~TABLE_CELL_WRAP_START~~ * Presentation by Peter Fraser, single cell HI-C method. * Update on sub working groups: * PLAC-seq/HiChIP: (Miao Yu) * single cell Hi-C (Burak) * other sub working groups ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-03-12-2018|Meeting minutes]]\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZjUyMDBkZTk0NTZjZmI4|Presentation for Single cell Hi-C from Peter Fraser Lab]] ~~TABLE_CELL_WRAP_STOP~~| |4-9-2018|~~TABLE_CELL_WRAP_START~~ * Discussion and approval of Single Cell Hi-C protocol ([[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyYTcwMmY0ZjUxODY0NzA4|link]]), presented by Dr. Peter Fraser a month ago. * Update from sub-working group - PLAC-seq/HiChIP (Miao Yu). Different library prep will not affect data quality. * Update from sub-working group - single cell Hi-C (Burak Alver). * Update from sub-working group - allele specific Hi-C (Burak Alver). * Other businesses for future OMICS sessions ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-04-09-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |5-14-2018|~~TABLE_CELL_WRAP_START~~ * Overview of TSA-Seq method (Andrew Belmont’s research group). ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-05-14-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |6-11-2018|~~TABLE_CELL_WRAP_START~~ * Presentation on DamID protocol and data standard by Tom van Schaik (Bas van Steensel lab). ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:protocols:damid|Wiki page for DamID]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-11-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |6-25-2018|~~TABLE_CELL_WRAP_START~~ * Discussion on CUT&RUN by Steven Henikoff ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-25-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |7-23-2018|~~TABLE_CELL_WRAP_START~~ * Discuss and vote on the DamID protocol (see link [[4dn:phase1:protocols:damid|here]]). This was presented on June 11th. * Discussion and vote on the Cut&Run protocol (see link [[https://www.google.com/url?q=https://www.nature.com/articles/nprot.2018.015.epdf?author_access_token=vf_ylGdH8oTFIbGYdyahH9RgN0jAjWel9jnR3ZoTv0NOQV_YOinFX53TT-yN_6ziKCqbazelkV5TLOcj4FgNB72aCjfEhYgiGP0HE3gHZJbRtWNmNoZwyH7Y6HToKMfQ&sa=D&sntz=1&usg=AFQjCNECGEGq02z8erEG0gwEFw9TpUF8cA|here]]). This was presented on June 25th. * Allele-specific alignment of HiC reads. (Burak Alver). ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-07-23-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |8-13-2018|~~TABLE_CELL_WRAP_START~~ * PLAC-seq data analysis by Ivan Juric and Miao Yu. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-08-13-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |9-10-2018|~~TABLE_CELL_WRAP_START~~ * Update on PLAC-seq/HiChIP standard discussion (Miao Yu) * Future OMICS discussion and presentation sign ups. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-09-10-2018|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |11-19-2018 |~~TABLE_CELL_WRAP_START~~ * Presentation on optimization and comparison of PLAC-seq and HiChIP protocols (Ren lab/Miao Yu). * Discussion. ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-11-19-2018|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozZWVjOGY4YTk0Y2RhN2M1|Presentation by Miao Yu.]]~~CKG_TABLE_NBSP~~"Optimization and Comparison of PLAC-seq and HiChIP protocols" ~~TABLE_CELL_WRAP_STOP~~| |1-28-2019 |~~TABLE_CELL_WRAP_START~~ * PLAC-seq/HiChIP discussion update (Miao Yu) * Single cell Hi-C sub-working group (Burak / Bill) * Plan out the OMICS working group for 2019 ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-28-2019|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |2-25-2019 |~~TABLE_CELL_WRAP_START~~ * Schedule for future presentations * Need to look at the SC minutes to see which protocols are in production, and approved. (DNase-HiC, in situ HiC, DamID, repli-seq, ChIA-PET) * Any additional omic standards to be discussed? ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |3-25-2019 |~~TABLE_CELL_WRAP_START~~ * Update on PLAC-seq / HiChIP protocol ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[4dn:phase1:working_groups:omics_data_standards:minutes-03-25-2019|Meeting minutes]] Presentation by Miao Yu ~~TABLE_CELL_WRAP_STOP~~| |~~TABLE_CELL_WRAP_START~~ === 2020 Meetings === ~~TABLE_CELL_WRAP_STOP~~ ||| |3-23-2020 |~~TABLE_CELL_WRAP_START~~ * Review protocols recommended for 4DN SC ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/document/d/1t3fxUTzABezu5fxhH_iAMq1szaojHD8FdUFRs9UWGcI/edit?pli=1|Meeting minutes]] ~~TABLE_CELL_WRAP_STOP~~| |4-27-2020 |~~TABLE_CELL_WRAP_START~~ * Review last month’s minutes and action plan. * Presentation on comparison of ChIA-PET/HiCHIP/PLAC-seq (Dr. Xiaotao Wang from Dr. Feng Yue’s group) ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://docs.google.com/document/d/1WzKl4ACWO1lxQrMTmEFdF_8N51DArW4-aIMbjeh7siw/edit?pli=1|Meeting minutes]] [[https://wiki.4dnucleome.org/_media/4dn:working_groups:omics_data_standards:4dn-pulldown-based-0427.pptx|Presentation by Dr. Xiaotao Wang]] ~~TABLE_CELL_WRAP_STOP~~| |6-22-2020~~CKG_TABLE_NBSP~~ |~~TABLE_CELL_WRAP_START~~ * Meeting minutes~~CKG_TABLE_NBSP~~ ~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~ [[https://mail.google.com/mail/u/0?ui=2&ik=ed374f079d&attid=0.1&permmsgid=msg-f:1670220830497479983&th=172dd0ff02429d2f&view=att&disp=safe|Discussion on HiChIP/PLAC-seq protocol]]~~CKG_TABLE_NBSP~~ ~~TABLE_CELL_WRAP_STOP~~| ===== Mailing list ===== The mailing list to use for communication in this Working Group is . Emails sent there will go to everyone on the list. Replying to an email from the list will also send it to everyone in the list. ===== Calendar ===== {{url>https://calendar.google.com/calendar/embed?src=6it3bntuu76dtpe4odqmoke3l0%40group.calendar.google.com 800,400 noborder|4DN OMICS WG Calendar}} ---- {{medialist>4dn:working_groups:omics_data_standards:}}