mC compartment, Genome Partition, Dynamic Cell Cluster Regrouping, Call DMR

[lhqing]

221118 Second pass DMR calling

• [x] Call DMR by major region a. All DMR from genome partition and dynamic cluster merge, using all cell types b. Each major region DMR using major region clusters (defined in RS2 analysis)
• [x] merge DMR and DMS a. concatenate all DMR/DMS, remove identical items b. for DMR, merge overlapped region into DMR groups, report group, but use individual DMR in correlation analysis and select the best to represent group
• [x] redo motif scan
• [x] redo DMR mC RegionDS
• [x] redo DMR ATAC RegionDS
• [ ] DMR status (hypo hyper)
• [ ] DMR motif hits
• [x] Update wmb api to add new DMR info

DMR Stats

• Total DMS: 19774760
• Total CpG: 43735100
• DMS / CpG %: 45.21%
• Total DMR Groups: 2564356
• Total DMR Group length mean, std: 189.6, 356.1
• Total singleton DMR Group: 1349228, 52.6%
• Total non-singleton DMR Group length mean, std: 358.5, 425.2
• Total DMR Group length and % of genome: 486177776, 18.5%
• Total DMR Group +/-100bp length and % of genome: 1255484576, 47.7%
• Total DMR regions: 8075960
• Total DMR Group length mean, std: 172.6, 290.8
• Total singleton DMR Group: 4662911, 57.7%
• Total non-singleton DMR Group length mean, std: 297.5, 331.0

First pass DMR calling

• [x] mCG all cluster compartment gs://ecker-hanqing-analysis/220906-genome-partition-and-dynamic-group
• [x] Get genome 100kb bin compartment gs://ecker-hanqing-analysis/220906-genome-partition-and-dynamic-group
• [x] Dynamic cell cluster regrouping within each compartment gs://ecker-hanqing-analysis/220911-dynamic-regroup
• [x] Call DMR in each compartment # this is the final pipeline used to call DMR gs://ecker-hanqing-analysis/220923-complete-dmr-pipeline
• [x] Evaluate DMR performance, finalize parameter

BaseDS API

• [x] DMS to DMR
• [x] Generate Bigwig
• [x] Generate BED bgzip/tabix
• [x] Generate JBrowse function, auto setup a config file to view in JBrowse
• [x] Setup default JBrowse config

[lhqing]

One example L2 | DissectionRegion | Partition Group PC1 | PC2 | PC3

[lhqing]

final group distance_cutoff = 0.2

[lhqing]

1.8M DMR in total, including DMS=1 pair

Template example: gs://ecker-hanqing-analysis/220923-complete-dmr-pipeline/0/0/template 01.dynamic_cluster_regroup.ipynb 02.call_dms.ipynb 03.call_dmr.ipynb

[lhqing]

Get DMR RegionDS from wmb.cemba

For the motif scan and hits see https://github.com/lhqing/whole_mouse_brain/issues/24#issuecomment-1260166826