https://wiki.4dnucleome.org/ 2026-04-19T03:30:28-0700 https://wiki.4dnucleome.org/ https://wiki.4dnucleome.org/_media/wiki:favicon.ico text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-01-08-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 01-08-2018 Update on the sub-working group focusing on PLAC-seq standard (Miao Yu) PLAC-Seq experimental protocols have been finalized and tested by several groups. Antibody selection protocols have been discussed. It is very crucial to demonstrate the specificity of antibody. Since ENCODE has an extensive protocol for antibody already, the sub working group decided to adapt the protocol. Antibodies should be tested and recorded by batches in this case. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-01-09-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 01-09-2017 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 text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-01-22-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 01-22-2018 Agenda * 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. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-01-28-2019?rev=1745364087&do=diff 4DN OMICS Standards Working Group 1/28/2019 Agenda * PLAC-seq/HiChIP discussion update (Miao Yu) * Last November, we had a discussion/presentation focusing on IP efficiency, reads overlapping protein binding sites * Since then, different batch of antibodies have been tested (K27ac, CTCF) for PLAC-seq. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-02-12-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 02-12-2018 Agenda * Updates on the sub-working groups. * Potential feedbacks on the SPRITE protocol. * Scheduling of additional OMICS protocols for future discussion. Updates on the sub-working groups Two of the subgroups are discussing some of the protocols, such as PLAC-Seq, Hi-Chip, Single cell Hi-C data standards and SPRITE (by Mitch Guttman). text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-02-13-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 02-13-2017 Issues of ChIA-PET standards: * Are ChIA-PET data are going to be produced? How many of them will be? * What are the parameters about QC or others that are needed for ChIA-PET? These two questions will need to be addressed by Dr Yijun Ruan for confirmation. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-02-25-2019?rev=1745364087&do=diff Agenda - * Schedule for future presentations * March 25: PLAC-seq/HiChIP standard presentation by Miao Yu * May 27th: GAM standard presentation by Ana Pombo lab * To be confirmed - in situ ChIA-PET from Ruan lab * Feature maps from Hi-C datasets text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-02-26-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 02-26-2018 Agenda: Sub working group updates Allele specific sub working group. There are three problems that have been discussed within the sub working group: * Phasing and what reference assembly should be use. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-02-27-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 02-27-2017 Summary * Recommendations for Hi-C standards were approved by DCIC * -ChIA-PET and PLAC-seq protocols drafted, will need to be approved by SC * -to find high order interactions, require new methods and discussion text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-03-12-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 03-12-2018 Agenda * Presentation by Peter Fraser, single cell HI-C method. \(protocol attached). - Update on sub working groups: - PLAC-seq/HiChIP: \(Miao Yu) * single cell Hi-C (Burak) * other sub working groups text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-03-13-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 03-13-2017 Repli-seq \ 1.-Resolution of replication timing experiments: Biological limitation Peaks within domains Boundary resolution \ 4DN Goal: define what resolution means \ 2.- E/L method Different cell lines have different data qualities and resolutions as well \ text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-03-25-2019?rev=1745364087&do=diff Update on PLAC-seq/HiChIP protocol * QC metrics * Recommended antibodies * Crosslinking conditions QC Metrics * Hi-C - digestion/ligation efficiency, noise level * IP - enrichment performance * Library preparation - complexity All three aspects have both a qualitative detection methods and quantitative detection method (with shallow sequencing) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-04-09-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 04-09-2018 Agenda * Discussion and approval of Single Cell Hi-C protocol (attached), 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? ===== Vote for motion to app… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-04-10-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 04-10-2017 AGENDA: * Agenda has changed today since the presenters (for microC protocol) were not ready for today’s meeting. * This call will be used to cover issues that were left open for OMICS discussions, such as ‘Hi-C data standards’. We will highlight things that are not clear. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-04-24-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 04-24-2017 Mapping in Hi-C Four groups presenting: Aiden, Mirny, Ren and DCIC Juicer from Aiden Lab Pipeline * Align reads as Single-end in parallel with bwa * Chimeric handling, merge sorting * “Wobble” removing duplicates text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-05-08-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 05-08-2017 Hi-C Data Processing and Analysis Hi-C Read Alignment and Data Standards (Please refer to Soo Lee’s slides) Reporting of chimeric alignment (-5 and -M flags) “”“” “” Single-end vs. Paired-end mode text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-05-14-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 05-14-2018 4DN OMICS Minutes, May 14, 2018 \ 1.- Overview of TSA-Seq method (Andrew Belmont’s research group). \The information about this work is in the following pre-print -bioRxiv preprint: https://www.biorxiv.org/content/early/2018/04/25/307892 \ Tyramide Signal Amplification (TSA) -Seq method principles: Is a genomic proximity mapping method that can measure chromosome distance at any chromosome loci to particular nuclear compartment and transform that… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-05-22-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 05-22-2017 05-22-2017 4DN OMICS MINUTES Next meeting June 12th, 2017 AGENDA: * Repli-Seq protocol and data standards (We have a final version of the protocol and standards from Dr. David Gilbert, and will have a vote on this). \ text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-05-23-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 05-23-2016 High-quality genome-wide contact mapping A standardized in situ Hi-C protocol may need discussion when further results are available in the participating labs (such as the ones with the quick-cutters). text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-11-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-11-2018 Agenda Presentation on DamID protocol and data standard by Tom van Schaik (Bas Van Steensel lab). DamID Protocol and Data Standard * Lentiviral transductions, followed by DNA isolation * Methyl-specific library prep text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-12-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-12-2017 AGENDA * Discussion of HG38 vs. HG19. \Which version should be used by 4DN? Pros and cons * Concepts of chromatin loops, domains. \Collection of opinions. Hg38 vs hg19 and other issues regarding to references text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-13-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-13-2016 Experiment Procedures, meta-data * Finalizing the experiment protocol. Derive the Hi-C standard from existing, published in situ Hi-C protocols. Determine what is variable and what should be unified and precise documentation of such variables text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-25-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-25-2018 AGENDA CUT and RUN Presentation by Steven Henikoff Features of the CUT and RUM method: * Limit digestion of targeted fragments * Can profile insoluble proteins. * Give high resolution TF mapping and prefers one surface of DNA duplex. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-26-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-26-2017 AGENDA: * Discussion of norm test (Burak/DCIC). * Finishing up discussion of hg19 vs hg38, * Compartment calling, * Voting on specific quantitative thresholds for successful hic experiments. * Concepts of chromatin loops, domains. \__(if time permits) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-06-27-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 06-27-2016 Determine Experimental Protocol * Create Protocol link to be public in the 4DN portal * Make a recommendation working group about decision and present in the steering committee * Variation in the protocol are expected And additional meetings to decide variations in the protocol text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-07-10-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 07-10-2017 Comparison of normalization methods (Slides by Burak et al. available on wiki to explore different normalization schemes) * DCIC has followed through workflows and can now present normalization results in HiGlass and Juicer (links in Slides) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-07-23-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 07-23-2018 Agenda * Discuss and vote on the DamID protocol (see link here). This was presented on June 11th. * Discussion and vote on the Cut&Run protocol (see link here - https://www.nature.com/articles/nprot.2018.015.epdf?author_access_token=vf_ylGdH8oTFIbGYdyahH9RgN0jAjWel9jnR3ZoTv0NOQV_YOinFX53TT-yN_6ziKCqbazelkV5TLOcj4FgNB72aCjfEhYgiGP0HE3gHZJbRtWNmNoZwyH7Y6HToKMfQ). This was presented on June 25th. * Allele-specific alignment of HiC reads. \__(Bura… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-07-24-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 07-24-2017 Agenda: * Discussion an updated ChIA-PET protocol and guideline (Yijun Ruan) * Nomination of additional OMICS protocols to be discussed in the OMICS WKG. * Update on HI-C normalization test (Burak Alver) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-07-25-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 07-25-2016 * Matrix Formats and intermediate formats to facilitate module swapping (mapping, etc) * FASTQ is definitely needed as the initial raw data * Discuss over which format should be the candidate * text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-08-08-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 08-08-2016 Discuss about data format * Benchmark results * Two data sets: lower resolution and larger resolution query for datasets with different sizes. Genome wide normalization for 1kb * Usability test from people not familiar to any of the formats to see whether they are easy to use text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-08-13-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 08-13-2018 AGENDA 1.- PLAC-seq data analysis by Ivan Juric and Miao Yu. INTRODUCTION * PLAC-Seq technology detect 3d interactions across the genome * There are multiple steps in PLAC-Seq, some of them happen in nucleus and some of them happen after that, such as restriction enzyme cutting, ligation, sonication, DNA purification and pull down and finally we end with paired reads and sequencing. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-08-14-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 08-14-2017 OMICS WG MEETING 08-14-2017 \ Agenda: \ * Continue discussion an updated ChIA-PET protocol and guideline (Yijun Ruan) * A proposed DCIC HI-C processing pipeline (here). (Peter Park) \ DISCUSSION \ text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-08-22-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 08-22-2016 DCIC presentation about meta data (Powerpoint file available on WG wiki here) * Basic Experiment Metadata * Lab * Name, PI, Institute, ... * User * Name * Grant * Number, Title, … * Publication text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-08-28-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 08-28-2017 AGENDA * Continue discussion with ChIA-PET data analysis * Continue discussion DCIC proposal regarding Hi-C visualization and process pipeline ChIA-PET Experimental has been available to everyone right now and last time discussion was visualization. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-09-10-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 09-10-2018 Agenda * Update on PLAC-seq/HiChIP standard discussion (Miao Yu) * Future OMICS discussion and presentation sign ups. \__ Update on PLAC-seq/HiChIP standard In previous discussions the pipeline for PLAC-seq/HiChIP has been discussed. The protocol and software has been published on bioRxiv and Github as well. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-09-12-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 09-12-2016 Usability study for different file formats. * Members (grad students and postdocs) in labs within 4DN are drafted to survey their opinion on using both formats. * Reports can be seen here on Google Docs: text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-09-26-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 09-26-2016 Omics Year 1 Report by Bing Ren Achievements * Common experiment protocol * Data file formats Goals for Year 2 * Data standards for Hi-C and ChIA-PET * Quality metric for chromatin organization features text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-10-09-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 10-09-2017 The agenda items are: \ 1. Summary of action items from the Consortium meeting \ \ Briefly, we identified a list of OMICS technologies for discussion by the OMICS group, and developed a general procedure for the discussion of each technique. \ \ 2. \ text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-10-23-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 10-23-2017 DCIC would like to prioritize the finalization a few standards including single cell Hi-C, allele specific Hi-C and other technologies. * Single cell Hi-C * We would need to get people who work on those technologies to agree upon the standard so that when people are submitting the data the standards can be followed. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 10-24-2016 Finalize recommendations on the Hi-C data standard, and particularly regarding sequencing depth, replicate number, and other criteria required for data submission. Replicates * Do we need a minimum data requirements (like number of replicates) to ensure the quality of results? text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-11-13-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 11-13-2017 Agenda * DNase-HiC protocol (Vijay Ramani from Jay Shendure lab) * Discussion * Single cell combinatorial indexing Hi-C protocol (sciHi-C) \__ Slides will be available at the link on 4DN wiki > Omics Working Group page. There will be a 30-day period when people can comment on the protocol and Vijay would be able to address those comments. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-11-14-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 11-14-2016 * 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: text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-11-19-2018?rev=1745364087&do=diff Omics Data Standards WG - Minutes 11-19-2018 Agenda * Presentation on optimization and comparison of PLAC-seq and HiChIP protocols (Ren lab/Miao Yu). * Discussion. Presentation on optimization and comparison of PLAC-seq and HiChIP protocols (Slides are available at text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-11-27-2017?rev=1745364087&do=diff Omics Data Standards WG - Minutes 11-27-2017 Agenda * 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 text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-11-28-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 11-28-2016 Agenda: * Final data standard for Hi-C. Submitted to steering committee and waiting for reply * Discussion of ChIA-PET experimental and data standards (Yi-jun Ruan and group). Detailed protocols will be published in Nature Protocols (Li et al.), mapping and visualization procedures will be published in Genome Research (Szataj et al.) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-12-12-2016?rev=1745364087&do=diff Omics Data Standards WG - Minutes 12-12-2016 Definition of loops for interaction contacts * Loop definition presented by Suhas Rao * Loops in chromatin will show a peak in a contact map * However, other features (such as domain/compartment structures) may interfere and needs to be accounted for in the model text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:working_groups:omics_data_standards:minutes-for-2-22?rev=1745364087&do=diff Omics Data Standards WG - Minutes for 2-22 Minutes recorded by Erez Lieberman Aiden. Apologies to all if I did not do justice to everything that was said! Minutes: 1) Uniform processing of data Data Serialization Everyone agrees that there should be a uniform pipeline