====== Data Analysis ======

<font 20px/inherit;;#e74c3c;;inherit>**The mailing list for the working group has been changed. Please use [[analysis@4dnucleome.org]] from now on as the new mailing list address.**</font>

===== Introduction =====

This is the introduction for each working group, it could be a brief summary of aims, objectives or other things.

===== Mission =====

The Analysis Working Group aims to identify, select, and if necessary implement computational methods for uniform processing and subsequent integration of the data produced by the 4DN consortium. AWG will also aim to identify outside data sets and tools that would benefit integrative analysis of 4DN data. While uniform processing and integrative analyses may not be possible for many of the data types being generated by the 4DN, AWG hopes to benefit the consortium by sharing the analysis expertise of individual teams through detailed presentations, discussions of common tools and data formats.

===== Documents =====

  * [[https://docs.google.com/document/d/1FTa1Z-LhTvQ96EtNkl4ziOX-xE6WvMuco_97Eg6Pwas/edit#|4DN DAWG HiC Pipeline Planning Document]]

===== Meetings =====

<font 20px/inherit;;#e74c3c;;inherit>**From March 1, 2018, the meetings of JAWG and DAWG merge together to the weekly 4DN JAWG/DAWG Meeting. The 4DN JAWG/DAWG Meeting is on every Thursday at 1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time).**</font>

You can use email address <meeting-4dn-dj@4dnucleome.org> to send emails to all the JAWG/DAWG meeting members.

All the meeting information are listed on JAWG wiki page. Click to JAWG wiki page to find agenda and notes.

===== WebEx Meeting Information =====

<font 20px/inherit;;inherit;;inherit>**Weekly Call - 4DN JAWG/DAWG Meeting Every Thursday（from March 1, 2018)**</font>

**1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time) **

[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m8ea943b4f866758ce61e412a002a8a95&sa=D&sntz=1&usg=AFQjCNF6uGcS20RnYEw3eNQCt5LdpcpmcQ|Click here to Join WebEx meeting]]\\ Meeting number: 805 283 801\\ Meeting password: uJe93m63\\ Host key: 347076

**Join by phone**\\ +1-415-655-0002 US Toll

Access code: 805 283 801

<font inherit/inherit;;#2980b9;;inherit>**WEBEX EMERGENCY CONTACT INFORMATION:**</font>

<font inherit/inherit;;#2980b9;;inherit>**KATE RIVERA**</font>

<font inherit/inherit;;#2980b9;;inherit>**858-822-1626 (OFFICE)**</font>

===== Meetings =====

\\ **1/13/2016**
  * **Links: **
      * [[https://docs.google.com/document/d/1rjYIXarELOkSWwDjsejTeWHotVKIlydGR2XIsI3Nyw4/edit?usp=sharing|google doc page]].
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6N2UxYWQ3Nzk0N2U2MTg4NQ|Additional notes]].

\\ **3/4/2016 **
  * **Agenda:**
      * Dekker lab HiC pipeline - Bryan Lajoie
  * **Links:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MmU1ZjMxM2ZlOGFiMGU5NQ|presentation]].
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NjNjNTAzYzAzZjI1MGZhZA|Some notes]]

**4/26/2016**
  * **Agenda:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Presentation on Hi-C quality and reproducibility metrics]] by Gurkan Yardimci from Bill Noble's group.
  * **Links:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Slides]].
      * [[https://docs.google.com/document/d/1Wojo6GG0VxXx17heUH9r1idltQlQV_718A0Aq-XvtN4/edit?usp=sharing|Additional notes.]]

**7/20/2016**

**Agenda:**
  * AWG+OMICS call. Presentations on loop detection from Erez Lieberman and [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/data-analysis-wg/Gold Standard Discussion Ren 072016.pptx?attredirects=0|Bing Ren]]'s groups.

**Links:**
  * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/AWG+OMICS joint call  benchmarking  loop detection-20160720 1629-1.arf&sa=D&sntz=1&usg=AFQjCNGi9pT8824uLCPV3VP_zGzftxV20w|Webex recording]].
  * [[https://docs.google.com/document/d/193FF2DJklhoBf7-bf0UgYeBeKkB2ThfffGxi9JY2WGw/edit|Minutes]].

**8/3/2016**
  * **Agenda:**
      * AWG+OMICS call. Presentation from Yijun Ruan's group
  * **Links:**
      * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/OMICS+AWG call 2  loop-based benchmarking-20160803 1600-1.arf&sa=D&sntz=1&usg=AFQjCNH5128cbaaySVTTM7AUfbQP8qn24A|Webex recording]].

**9/29/2016 **
  * **Links:**
      * [[https://docs.google.com/document/d/18meAIDn-m5j5dITktPiq7IW1tT9VoLigZkqILJoeSCE/edit?usp=sharing|Minutes]].

**1/26/2017 **
  * **Agenda:**
      * HiC reproducibility metrics - Gurkan Yardimici from Bill Noble's group.
  * **Links:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MTczMjE1ZDY1ZmZhNDcw|Slides]].

**3/23/2017**
  * **Agenda:**
      * Presentation by DCIC on uniform pipeline status and plans.
  * **Links:**
      * [[https://drive.google.com/file/d/0B6cuZNSltxB9Z2FFdHBvR2FhYkE/view|Slides]].
      * [[https://docs.google.com/document/d/1FTa1Z-LhTvQ96EtNkl4ziOX-xE6WvMuco_97Eg6Pwas/edit#|Google Doc]].
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=4ec05ba389507b37a3391145fb00f64d&sa=D&sntz=1&usg=AFQjCNH30uLLcUMxUN7SFdphnfonvZsnFQ|Webex recording]].

**4/6/2017 **
  * **Agenda:**
      * Presentation by Michael Sauria (James Taylor lab) on Hi-C reproducibility analysis
  * **Links:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyNDc1YzM2ZmY4ODRhOTdl|Slides]].
      * [[https://docs.google.com/document/d/1ASbJWYKiQVkGczmSdx4m760UL-r4hoF8v6Fcj_rmYx8/edit?usp=sharing|Google Doc]].

**4/20/2017**
  * **Agenda:**
      * DCIC updates / alignment (10minutes)
      * Presentation by Ren lab on Normalization (20min)
      * Discussion (10 minutes)
  * **Links:**
      * [[https://docs.google.com/document/d/16JFF_1IoEfmp8ns8kVhxK9n1eexENhv26lSgTA_96Ws/edit?usp=sharing|Minutes.]]
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=f00ca90cefe175a0493d6708b78cb2b8&sa=D&sntz=1&usg=AFQjCNGXxgex_vvdyOZVwEGipjcEoG-96A|Webex recording.]]

**5/4/2017**
  * **Agenda:**
      * DCIC updates (5minutes)
      * Presentation by Aiden lab on Normalization (20min)
      * Presentation by Mirny lab on Normalization (20min)
      * Discussion: what is needed for consensus? (15min)
  * **Links:**
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=f00ca90cefe175a0493d6708b78cb2b8&sa=D&sntz=1&usg=AFQjCNGXxgex_vvdyOZVwEGipjcEoG-96A|Recording.]]

**5/18/2017**
  * **Agenda:**
      * Presentation by Francesco Ferrari on TAD callers
  * **Links:**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0OGIxZDFiOTQ4NmY1MmI4|Slides]].
      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170518|DAWG Meeting Notes 20170518]].
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=179d1cdde5f4241f3b962f58f7b2c971&sa=D&sntz=1&usg=AFQjCNE942yNVAl2Sgg0mPlktnz5m3-d3w|Recording]].
      * [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/data-analysis-wg/Ferrari_TADcalls.rar?attredirects=0&d=1|TAD calls.]]

**6/1/2017**
  * **Agenda:**
      * Read filtering I: Mirny lab.
  * **Links:**
      * [[https://docs.google.com/presentation/d/1oZDoFMEFKz8JQUy-hx4roWcU_zP_9lzp2FwRuROkWEc/edit#slide=id.p|Slides]].
      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170601|DAWG Meeting Notes 20170601]].
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=fc5b4225a0e391dd0ba2af58c1ff9a16&sa=D&sntz=1&usg=AFQjCNHTzMaG1VOA-T139mcvo2l8KAo1YA|Recording]].

**6/15/2017**
  * **Agenda**
      * DCIC updates
      * Read filtering II
  * **Links**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyYzJmNzYyZjJlMWZkZTg1|Slides]].
      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170615|DAWG Meeting Notes 20170615]].

**7/13/2017**
  * **Agenda**
      * Continuing on: Presentation by Francesco Ferrari on TAD callers
      * Please write to Peter_Kharchenko@hms.harvard.edu if you would like to present
  * **Links**
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=c4a1d3568d4d50315b85220c44f3a9bb&sa=D&sntz=1&usg=AFQjCNH0DGRrtHz7xvOvac43z3FgaC5XlQ|Recording.]]

**8/3/2017**
  * **Agenda**
      * TAD Callers: continued discussion
      * Visualization of TADs
        * Peter Kerpedjiev (Gehlenborg lab) - HiGlass
        * Neva C Durand (Aiden Lab) - Arrowhead/Juicebox
  * **Links**
      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2ZDgyYzEwYTdiNjEwNGUx|Arrowhead Slides]].
      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170803|DAWG Meeting Notes 20170803]].
      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=920d2ead6e130d3560c557271acea7cc&sa=D&sntz=1&usg=AFQjCNGyIM_k4bR0ZbsOqKYA0Sw7ORcMZQ|Recording]].

**9/7/2017 **
  * **Agenda**
      * Defining contact domains: CTCF and cohesion depletion
        * Mirny Lab
        * Aiden Lab

===== Members (original list) =====

<font 20px/inherit;;inherit;;inherit>Co-Chairs:</font>

<font 20px/inherit;;inherit;;inherit>Peter Kharchenko, <peter_kharchenko@hms.harvard.edu>
William Noble, <wnoble@uw.edu></font>

<font inherit/inherit;;inherit;;#e74c3c>Insert data analysis members spreadsheet</font>

**Program Staff**

Weizhong Chen, PhD <wec125@eng.ucsd.edu>

This can be a list of all other working members in the working group.

===== Mailing list =====

The mailing list to use for communication in this Working Group is <analysis@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=l83jh4t35tpd46ad6dq822ck78%40group.calendar.google.com&ctz=America%2FLos_Angeles 800,400 noborder|4DN Data Analysis WG Calendar}}