###### tags: `Sprint Diary` # 4DN2 SPRINT DIARY - Q1S1 ## 17 Jan. 2023 / 10:00 AM ## Timeline ![](https://i.imgur.com/iyBfzGO.png) Attendees: * Nezar @nvictus * Vedat @VOY * Jiangyuan * Johan * Trevor ## Resources * Sprint Slides for Figures: https://docs.google.com/presentation/d/15f1CvLSlRxAC3k5dvzhdoVkWNJnDLSb4ox_0HzxHKdk/edit?usp=sharing/ * Kanban Board: https://airtable.com/shrNznOkqe3JGugKK * Github: https://github.com/abdenlab/4dn2-sprints.git * Whiteboard: https://miro.com/app/board/uXjVPxut4LQ=/?share_link_id=732063246408 * Action Items: * Sprint Goals: ## Agenda Previous Items: * Planned: * Trajectories of RNAseq; Relationship to epigenetic compartmentalization. * Insulation Scores and Short range interactions, TADs, Hi-C Low dimensional features * ATAC-Seq peaks across the developmental stages. * In Progress: * Consolidated Epigenetic racks * Improvements on IPG Clustering * Dot calling for newly mapped Hi-C Lanes: * RNAseq: Pairwise DEx ~~* RNAseq: Clustering on the latent Space, Results from Sashata needs details.~~ * Sprint Items: 1. Dot calling for newly mapped Hi-C Lanes with Jiangyuan 2. Higlass and widgets with Trevor Parking Lot: 1. No parked items Notes: ## Plan ## Huddle Day Notes ### Morning * Dot Calling (Discussion with Jiangyuan and Johan) * Jiangyuan will do a comparison of the union lists prev vs current, e.g. Upset plots. * Johan will make a megamap with all conditions together for standard dot calling. * HiGlass (Trevor): * polish up `hg` for release and convert the current `higlass-python` repo. * Add boilerplate logic for jupyter-scatter integration to `hg`. * Release notes for `anywidget` * Expose higlass's Jupyter widget using `anywidget` and deprecate `higlass-widget` ### EOD (around 4pm) * Trevor: Blog post with widgets are on the way. * Jiangyuan: Dot-calling will compare union dots, For RNAseq DEx; some NF-core output was not integers. Might round up to the nearest integer. # Sprint Notes ### Trevor Released `anywidget` and blog post!!! CONGRATS!!! https://anywidget.dev/blog/introducing-anywidget ### Jiangyuan Figures on [Slack](https://4dn2-csg.slack.com/archives/C03S6H86WCT/p1674232991733099) and [Sprint Slides](https://docs.google.com/presentation/d/15f1CvLSlRxAC3k5dvzhdoVkWNJnDLSb4ox_0HzxHKdk/edit?usp=sharing/). He focused on clusters of enriched pixels at 10 and 5 kb resolutions separately (left and middle plots (first two)). Pixels in each cluster could be enriched in one or more conditions. I just combined all their enriched conditions to represent each cluster. The right plot is the original one. After I merged 5 and 10kb dot calls, I used bioframe.cluster(min_dist=None). 7089 common dots across all 5 stages vs 1537 is quite an improvement! Next step is to know how to select the brightest pixel in each cluster to represent the whole cluster as a dot (e.g., max sum or just max of max across 5 stages. #### Nezar's suggestion This is very encouraging! With the new 10kb clusters, the highest overlap is across all 5 stages. 7089 common dots vs 1537 before. I think it's also worth trying the approach @Johan Gibcus mentioned on Tuesday that was used in the Reed et al paper: standard dot calling on a composite Hi-C map off all conditions. @Johan Gibcus - were you able to make a mega-merged map from all 5 stages? This **might work best** because it directly yields a "union list" of dots after which we can score those individual dot positions across all conditions to decide if a dot is enriched in a condition or not.