Closed rdmorin closed 8 months ago
There is one larger region for PAX5 that is redundant with two smaller ones and should be removed (indicated below).
chr_name hg19_start hg19_end gene region regulatory_comment name size
chr9 37023396 37027663 PAX5 intron-1 intronic PAX5-intron… 4267
chr9 37369209 37372160 PAX5 distal-enhancer-1 enhancer PAX5-distal… 2951
chr9 37382267 37385854 PAX5 distal-enhancer-2 enhancer PAX5-distal… 3587
chr9 37395932 37409239 PAX5 distal-enhancer-3 enhancer PAX5-distal… 13307
chr9 37032576 37037704 PAX5 TSS-1 active_promoter PAX5-TSS-1 5128
chr9 37021323 37043181 PAX5 TSS-2 active_promoter-strong_enhancer PAX5-TSS-2 21858 #remove this
This is a trickier one to consolidate. Removing the larger region that encompasses the two others would mean no coverage for one place that is commonly mutated. Perhaps this large region should be split into three or four consecutive regions?
chr_name hg19_start hg19_end gene region regulatory_comment name size
chr9 37192080 37207549 ZCCHC7 intron-3 intronic ZCCHC7-intron-3 15469
chr9 37282092 37309161 ZCCHC7 intron-2 intronic ZCCHC7-intron-2 27069
chr9 37323113 37340687 ZCCHC7 intron-1 intronic ZCCHC7-intron-1 17574
chr9 37276495 37342191 ZCCHC7 intronic NA ZCCHC7-intronic 65696 #split up and remove redundant overlapping regions from above?
LPP has a few massive regions. I think these should also be split up. Perhaps one representing the "hottest" area and a few spanning the rest?
chr_name hg19_start hg19_end gene region regulatory_comment name size
chr3 187771678 187982852 LPP TSS-1 NA LPP-TSS-1 211174 # split into at least 3 regions
chr3 188377178 188491248 LPP intronic NA LPP-intronic 114070 #split into at least 3 regions
Another huge one that should probably be split up
chr_name hg19_start hg19_end gene region regulatory_comment name size
chr5 88131209 88206620 MEF2C TSS active_promoter MEF2C-TSS 75411
This is now fixed in this update but I will hold off to closing this issue until GAMBLR is set up to work with that designated data storage repo
The new setup is already tested for awhile without reported issues. Closing the issue as completed
There are redundant aSHM regions in our bundled set of regions. These need to be collapsed to the most representative one for each region to avoid double-counting etc. These should be flagged in the comments of this issue and someone needs to remove the redundant ones. This should really all be done using the "master" list that now lives in this repo.
To get things started, here's a few examples: