RDS with Chicago
library(Chicago)
kc0 = readRDS("humKer_Sub_D2D8_merge.Rds")
head(kc0@x)
write.table(kc0@x, file="1.bed")
1. Digest_Human_HindIII.6col_XY-4.bed -> Digest_Human_HindIII.6col.bed (add4_toChrXY.sh)
2. Enhc_Digest_Human_HindIII_ID_XY-4.bed -> Enhc_Digest_Human_HindIII_ID.bed (add4_toChrXY.sh)
3. humKer_Sub_D2D8_merge.Rds.gz -> D0_D2D8_merge_w_chrM.bed.gz (Chicago)
4. D0_D2D8_merge_w_chrM.bed.gz -> D0_D2D8_merge.bed.gz (remove_chrM.sh)
For bait-bait:
1. D0_D2D8_merge.bed.gz -> D0_D2D8_merge_BaitToBait.txt (get_baits.sh)
2. for D0_D2D8_merge_BaitToBait.txt
check_if_baits.ipynb - ALL SITES ARE BAITS!!!!!
3. D0_D2D8_merge_BaitToBait.txt -> D0_D2D8_merge_BaitToBait.bed (get_bed_from_IDs_txt.sh/get_bed_from_IDs_txt.py, get_bed_from_IDs_txt.ipynb)
4. D0_D2D8_merge_BaitToBait.bed -> D0_D2D8_merge_BaitToBait_intra.bed (get_intra.sh)
For enhancers:
1. Digest_Human_HindIII.6col.bed -> Enhc_Digest_Human_HindIII_ID.bed (get_enhc_digest_human_hind3.sh)
For bait-other
1. D0_D2D8_merge.bed.gz -> D0_D2D8_merge_BaitToOther.txt(get_bait-other.sh)
2. for D0_D2D8_merge_BaitToOther.txt
check_which_site_is_bait.ipynb - SITE1 IS BAIT!!!!!
3. D0_D2D8_merge_BaitToOther.txt -> D0_D2D8_merge_BaitToE.txt (get_baitToE.sh/get_baitToE.py using Enhc_Digest_Human_HindIII_ID.bed)
4. D0_D2D8_merge_BaitToE.txt -> D0_D2D8_merge_BaitToE.bed (get_bed_from_IDs_txt.sh/get_bed_from_IDs_txt.py, get_bed_from_IDs_txt.ipynb using Digest_Human_HindIII.6col.bed)
5. D0_D2D8_merge_BaitToE.bed -> D0_D2D8_merge_BaitToE_intra.bed (get_intra.sh)