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--- 4dn:phase1:working_groups:omics_data_standards [2019/09/06 10:56]
xiaoyi_cao
+++ 4dn:phase1:working_groups:omics_data_standards [2025/04/22 16:21] (current)
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 ====== Omics Data Standards ======
-<font 20px/inherit;;#e74c3c;;inherit>**The mailing list for the working group has been changed. Please use [[omics@4dnucleome.org]] from now on as the new mailing list address.**</font>
+**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 =====
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-**<font 20px/inherit;;#2980b9;;inherit>WEBEX EMERGENCY CONTACT INFORMATION:</font>**
+**<font 20px/inherit;;#2980b9;;inherit>WEBEX CONTACT INFORMATION:</font>**
-**<font 20px/inherit;;#2980b9;;inherit>KATE RIVERA</font>**
+Catherine Rivera-Noel [[oh@4dnucleome.org|]]
-**<font 20px/inherit;;#2980b9;;inherit>858-822-1626 (OFFICE)</font>**
 ===== Documents =====
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 [[https://docs.google.com/document/d/1wPQygR1at6ureVlO2Jp8J629l6WyWmIiWmUEs4aKi0s/edit?usp=sharing|minutes prepared by bing ren]]
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 |2-8-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * [[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]]
@@ Line 185: / Line 188: @@
   * [[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]]
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-[[:4dn:working_groups:omics_data_standards:minutes-for-2-22|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-for-2-22|Meeting minutes]]
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 |3-14-2016|~~CKG_TABLE_NBSP~~|~~CKG_TABLE_NBSP~~|
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-[[:4dn:working_groups:omics_data_standards:minutes-05-23-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-23-2016|Meeting minutes]]
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 |6-13-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Discussion of experiment protocols
   * Discussion of standard data formats
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-[[:4dn: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
+[[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
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 |6-27-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Determine experimental protocols
   * Discussion of meta-data
   * Discussion of data formats
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-06-27-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-27-2016|Meeting minutes]]
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 |7-11-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * [[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
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-[[:4dn:working_groups:omics_data_standards:minutes-07-25-2016|Meeting minutes ]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-07-25-2016|Meeting minutes ]]
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 |8-8-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[:4dn:working_groups:omics_data_standards:minutes-08-08-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-08-2016|Meeting minutes]]
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 |8-22-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[:4dn:working_groups:omics_data_standards:minutes-08-22-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-22-2016|Meeting minutes]]
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 |9-12-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * [[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)]]
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-[[:4dn:working_groups:omics_data_standards:minutes-09-12-2016|Meeting minutes ]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-12-2016|Meeting minutes ]]
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 |9-26-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * OMICS year 1 report
   * Dataset requirements (coverage, etc.)
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-[[:4dn:working_groups:omics_data_standards:minutes-09-26-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-26-2016|Meeting minutes]]
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 |10-24-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[:4dn:working_groups:omics_data_standards:minutes-10-24-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016|Meeting minutes]]
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 |11-14-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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]]
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-[[:4dn:working_groups:omics_data_standards:minutes-11-14-2016|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016|Meeting minutes]]
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 |11-28-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[:4dn:working_groups:omics_data_standards:minutes-11-28-2016|Meeting minutes]]\\ Presentation
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-28-2016|Meeting minutes]]\\ Presentation
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 |12-12-2016|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[:4dn:working_groups:omics_data_standards:minutes-12-12-2016|Meeting minutes]]\\ Presentation from Suhas Rao
+[[4dn:phase1:working_groups:omics_data_standards:minutes-12-12-2016|Meeting minutes]]\\ Presentation from Suhas Rao
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 |1-9-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozYTM1N2M2MzI4MDJkMWI|Draft ChIP-PET protocol (from Y Ruan)]]\\ [[:4dn:working_groups:omics_data_standards:minutes-01-09-2017|Meeting minutes]]
+[[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]]
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 |2-13-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-Presentation from Rongxin Fang\\ [[:4dn:working_groups:omics_data_standards:minutes-02-13-2017|Meeting minutes]]
+Presentation from Rongxin Fang\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-02-13-2017|Meeting minutes]]
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 |2-27-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[https://docs.google.com/spreadsheets/d/1eNajg-wroy9Ruj7xAj6i087nm-eM54ueFrBuP5m7JsU/edit?usp=sharing|Spreadsheet for tentative future topics and date]]\\ [[:4dn:working_groups:omics_data_standards:minutes-02-27-2017|Meeting minutes]]
+[[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]]
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 |3-13-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3OGQxYjE1YmU1NWUzNWYz|Slides for Repli-seq]]\\ [[:4dn:working_groups:omics_data_standards:minutes-03-13-2017|Meeting minutes]]
+[[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]]
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 |4-10-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MWQ2MjlkMDU4OTAzYjBi|DCIC Metadata Slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-04-10-2017|Meeting minutes]]
+[[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]]
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 |4-24-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Alignments of Hi-C
   * [[https://docs.google.com/a/broadinstitute.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozM2YzNjY3MDcyY2U1Njky|Read mapping]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-04-24-2017|Meeting minutes]]\\ [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2MmU5ZmEyNGM2OGY5MDJj|DCIC presentation]]
+[[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]]
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 |5-8-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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)]]
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-[[:4dn:working_groups:omics_data_standards:minutes-05-08-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-08-2017|Meeting minutes]]
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 |5-22-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 348: / Line 405: @@
   * Hi-C Read Alignment
   * Hi-C Normalization ([[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo5Zjg1ZWZiMTQ2NTYyNGQ|Slides]])
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-05-22-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-22-2017|Meeting minutes]]
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 |6-12-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Discussion of HG38 vs. HG19. Which version should be used by 4DN? Pros and cons
   * Concepts of chromatin loops, domains. Collection of opinions.
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-[[:4dn:working_groups:omics_data_standards:minutes-06-12-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-12-2017|Meeting minutes]]
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 |6-26-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Discussion of norm test (Burak/DCIC).
   * Finishing up discussion of hg19 vs hg38,
   * Compartment calling
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-[[:4dn:working_groups:omics_data_standards:minutes-06-26-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-26-2017|Meeting minutes]]
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 |7-10-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-[[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0N2M0MWNkNTlkYjFjM2Qw|DCIC update slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-07-10-2017|Meeting minutes]]
+[[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]]
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 |7-24-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
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-ChIA-PET updated protocol\\ [[https://docs.google.com/a/4dnucleome.org/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoxYWNiZWJlNmQ2MzEyOWUw|ChIA-PET slides]]\\ [[:4dn:working_groups:omics_data_standards:minutes-07-24-2017|Meeting minutes]]
+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]]
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 |8-14-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Continued discussion an updated ChIA-PET protocol and guideline (Yijun Ruan)
   * A proposed DCIC HI-C processing pipeline (Peter Park)
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[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:working_groups:omics_data_standards:minutes-08-14-2017|Meeting minutes]]
+[[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]]
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 |8-28-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Continue discussion with Chia-PET data analysis
   * Continue discussion DCIC proposal regarding Hi-C visualization and process pipeline
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-[[:4dn:working_groups:omics_data_standards:minutes-08-28-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-28-2017|Meeting minutes]]
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 |10-9-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * [[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.
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-[[:4dn:working_groups:omics_data_standards:minutes-10-09-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-09-2017|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |10-23-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 414: / Line 495: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-10-23-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-10-23-2017|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |11-13-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * DNase-HiC protocol (Vijay Ramani from Jay Shendure lab)
   * Discussion
   * Single cell combinatorial indexing Hi-C protocol (sciHi-C)
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-11-13-2017|Meeting minutes]]\\ Slides
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-13-2017|Meeting minutes]]\\ Slides
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |11-27-2017|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-11-27-2017|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-11-27-2017|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |1-8-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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.
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-01-08-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-01-08-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |1-22-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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.
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view|SPRITE protocol]]\\ [[:4dn:working_groups:omics_data_standards:minutes-01-22-2018|Meeting minutes]]
+[[https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view|SPRITE protocol]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-01-22-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |2-12-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Updates on the sub-working groups.
   * Potential feedbacks on the SPRITE protocol.
   * Scheduling of additional OMICS protocols for future discussion.
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-02-12-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-12-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |2-26-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 468: / Line 573: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-02-26-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-26-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |3-12-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn: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]]
+[[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]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |4-9-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 486: / Line 599: @@
   * 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
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-04-09-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-04-09-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |5-14-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 498: / Line 616: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-05-14-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-05-14-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |6-11-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 505: / Line 625: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:protocols:damid|Wiki page for DamID]]\\ [[:4dn:working_groups:omics_data_standards:minutes-06-11-2018|Meeting minutes]]
+[[4dn:phase1:protocols:damid|Wiki page for DamID]]\\ [[4dn:phase1:working_groups:omics_data_standards:minutes-06-11-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |6-25-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 512: / Line 634: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-06-25-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-06-25-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |7-23-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
-  * Discuss and vote on the DamID protocol (see link [[:4dn:protocols:damid|here]]). This was presented on June 11th.
+  * 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).
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-07-23-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-07-23-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |8-13-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 528: / Line 656: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-08-13-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-08-13-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |9-10-2018|~~TABLE_CELL_WRAP_START~~<WRAP>
   * Update on PLAC-seq/HiChIP standard discussion (Miao Yu)
   * Future OMICS discussion and presentation sign ups.
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-09-10-2018|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-09-10-2018|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |11-19-2018  |~~TABLE_CELL_WRAP_START~~<WRAP>
   * Presentation on optimization and comparison of PLAC-seq and HiChIP protocols (Ren lab/Miao Yu).
   * Discussion.
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn: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"
+[[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"
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |1-28-2019  |~~TABLE_CELL_WRAP_START~~<WRAP>
   * PLAC-seq/HiChIP discussion update (Miao Yu)
   * Single cell Hi-C sub-working group (Burak / Bill)
   * Plan out the OMICS working group for 2019
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-01-28-2019|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-01-28-2019|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |2-25-2019  |~~TABLE_CELL_WRAP_START~~<WRAP>
   * 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?
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-02-25-2019|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019|Meeting minutes]]
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
 |3-25-2019  |~~TABLE_CELL_WRAP_START~~<WRAP>
@@ Line 569: / Line 713: @@
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
-[[:4dn:working_groups:omics_data_standards:minutes-03-25-2019|Meeting minutes]]
+[[4dn:phase1:working_groups:omics_data_standards:minutes-03-25-2019|Meeting minutes]]
 Presentation by Miao Yu
 </WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|~~TABLE_CELL_WRAP_START~~<WRAP>
-===== Listserv =====
+=== 2020 Meetings ===
-The Listserv to use for communication in this Working Group is [[4DN-OMICS@list.nih.gov|]]. 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. [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/omicswg/Detailed Instructions on how to interact with the listserv - Omics.pdf?attredirects=0&d=1|Detailed Instructions on how to interact with the Listserv System are available - Omics]]
+</WRAP>~~TABLE_CELL_WRAP_STOP~~  |||
+|3-23-2020  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * Review protocols recommended for 4DN SC
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[https://docs.google.com/document/d/1t3fxUTzABezu5fxhH_iAMq1szaojHD8FdUFRs9UWGcI/edit?pli=1|Meeting minutes]]
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|4-27-2020  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * <font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit>Review last month’s minutes and action plan.</font></font>
+  * <font 12pt/inherit;;inherit;;inherit><font inherit/Calibri,sans-serif;;inherit;;inherit>Presentation on comparison of ChIA-PET/HiCHIP/PLAC-seq (Dr. Xiaotao Wang from Dr. Feng Yue’s group)</font></font>
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[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]]
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
+|6-22-2020~~CKG_TABLE_NBSP~~  |~~TABLE_CELL_WRAP_START~~<WRAP>
+  * Meeting minutes~~CKG_TABLE_NBSP~~
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|~~TABLE_CELL_WRAP_START~~<WRAP>
+[[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~~
+</WRAP>~~TABLE_CELL_WRAP_STOP~~|
+===== Mailing list =====
+The mailing list to use for communication in this Working Group is <omics@4dnucleome.org>. 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:}}

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