Comments (1)
petercombs
commented on July 26, 2024
Looks like this won't actually work, since we have exactly zero overlaps (even after converting data to the same reference coordinates):
$ bedtools closest -a kirchner.bed -b klein_all_hg38.bed -d | column -t
1 109274651 109275251 SORT1-flip 1 109895959 109896145 620709
1 109274652 109275251 SORT1 1 109895959 109896145 620709
1 109274652 109275251 SORT1.2 1 109895959 109896145 620709
1 155301395 155301864 PKLR-24h 1 151002805 151002988 4298408
1 155301395 155301864 PKLR-48h 1 151002805 151002988 4298408
1 209815790 209816390 IRF6 1 211616739 211616925 1800350
10 43086479 43087078 RET 10 71342543 71342725 28255466
10 46046244 46046834 MSMB 10 71342543 71342725 25295710
10 112998240 112998839 TCF7L2 10 100341257 100341443 12656798
11 5227022 5227208 HBB 11 1988198 1988384 3238639
11 5249805 5250078 HBG1 11 1988198 1988384 3261422
19 11089231 11089548 LDLR 19 7398818 7399004 3690228
19 11089231 11089548 LDLR.2 19 7398818 7399004 3690228
2 60494940 60495539 BCL11A 2 47074762 47074947 13419994
2 161238408 161238998 UC88 2 134457866 134458047 26780362
20 44355520 44355804 HNF4A 20 48373754 48373940 4017951
22 19723266 19723650 GP1BA 22 19892087 19892273 168438
5 1294989 1295247 TERT-GAa 5 1563189 1563375 267943
5 1294989 1295247 TERT-GBM 5 1563189 1563375 267943
5 1294989 1295247 TERT-GSc 5 1563189 1563375 267943
5 1294989 1295247 TERT-HEK 5 1563189 1563375 267943
6 396143 396593 IRF4 6 7137078 7137253 6740486
6 37807499 37808077 ZFAND3 6 36127549 36127734 1679766
7 156791119 156791604 ZRSh-13 7 99372645 99372831 57418289
7 156791119 156791604 ZRSh-13h2 7 99372645 99372831 57418289
8 127400829 127401428 MYCrs6983267 8 128176976 128177162 775549
8 127519270 127519732 MYCrs11986220 8 128176976 128177162 657245
9 97853255 97853854 FOXE1 9 114118163 114118348 16264310
X 139530463 139530765 F9 . -1 -1 -1
In some cases we get as close as 170kb, but that's not really the same thing, now is it.
from mpra_selection.
Related Issues (11)
- Decide what to do when there's not complete saturation of the mutagenesis HOT 1
- Merge Reconstructions doesn't work with snakemake on the cluster
- Think more closely about what to do with bases where we have data on deletions
- Make sure to process exonic enhancers differently HOT 2
- Deal with LINE elements HOT 3
- Deal with internal node if sequence same as parent
- Make changes to allow software to run more easily on different computers HOT 1
- BLAST can sometimes not return any hits in Rodents HOT 1
- Have some method to specify target ingroup HOT 1
- Come up with a figure or three on biological results HOT 2
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from mpra_selection.