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README-Hi-C.txt
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README-Hi-C.txt
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## coolers
#coolers used for insulation on fig1
/nl/umw_job_dekker/users/av90w/cooler/20210323_merge_more_lib_same/NT/CkoCT442-NT-pool.mcool
/nl/umw_job_dekker/users/av90w/cooler/20210323_merge_more_lib_same/IAA/CkoCT442-IAA-pool.mcool
## Pool HAP1 WT, NO TIR1 and TIR1
/nl/umw_job_dekker/users/av90w/cooler/20210408_merge_NO_TIR1_44/CkoC44-NO-TIR1-pool.mcool
/nl/umw_job_dekker/users/av90w/cooler/downsampling/Hap1-WT-combined-500000000.mcool
/nl/umw_job_dekker/users/av90w/cooler/downsampling/CkoCT442-NT-pool-500000000.mcool
/nl/umw_job_dekker/users/av90w/cooler/downsampling/CkoCT442-IAA-pool-500000000.mcool
## Pool HAP1 WT and PolII degron NT and IAA
/nl/umw_job_dekker/users/av90w/cooler/Hap1-WT-combined.mcool
/nl/umw_job_dekker/users/av90w/cooler/downsampling/PTB2539-NT-pool-800000000.mcool
/nl/umw_job_dekker/users/av90w/cooler/downsampling/PTB2539-IAA-pool-800000000.mcool
# HAP1 mother cell line
# to merge together to have more reads? (both sets)
#set #1
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-NT__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA4H__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA24H__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA48H__hg19.hg19.mapq_30.1000.mcool
#set #2
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-NT-R2-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA4H-R2-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA48H-R2-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA4HW4-R1-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA4HW24-R1-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library/Hap1-WT-IAA4HW48-R1-T1__hg19.hg19.mapq_30.1000.mcool
#CTCF degron asynchronous
NT
/nl/umw_job_dekker/users/av90w/distiller-run/20200325_mapping_for_dot_calling_cispercent/results/coolers_library/CkoC442-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
IAA
/nl/umw_job_dekker/users/av90w/distiller-run/20200325_mapping_for_dot_calling_cispercent/results/coolers_library/CkoC442-IAA48H-R1-T1__hg19.hg19.mapq_30.1000.mcool
#DDX55 clones
DDX55sg2B NT
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-DDX55sg2-B-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
DDX55sg2B IAA
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-DDX55sg2-B-IAA-R1-T1__hg19.hg19.mapq_30.1000.mcool
DDX55sg27 NT
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-DDX55sg2-7-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
DDX55sg27 IAA
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-DDX55sg2-7-IAA-R1-T1__hg19.hg19.mapq_30.1000.mcool
#AAVS1 clone
NT
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-AAVS1sg2-4-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
IAA
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library/CkoCT442-AAVS1sg2-4-IAA-R1-T1__hg19.hg19.mapq_30.1000.mcool
# locations of the pooled DDX55 and TAF5L clone mcool:
/nl/umw_job_dekker/users/av90w/cooler/20210413_merge_same_depth/CkoCT442-AAVS1-NT-pool.mcool
/nl/umw_job_dekker/users/av90w/cooler/20210413_merge_same_depth/CkoCT442-AAVS1-IAA-pool.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20190924_CTCF_screen_clones_morereads/results/coolers_library_group/DDX55-clones-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20190924_CTCF_screen_clones_morereads/results/coolers_library_group/DDX55-clones-IAA.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20190924_CTCF_screen_clones_morereads/results/coolers_library_group/TAF5L-clones-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20190924_CTCF_screen_clones_morereads/results/coolers_library_group/TAF5L-clones-IAA.hg19.mapq_30.1000.mcool
# locations of the siRNA DDX55 and TAF5L mcool:
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siCTRL-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siCTRL-IAA.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siDDX55-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siDDX55-IAA.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siTAF5L-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20191105_CTCF_screen_siRNA_replicates_withgroups/results/coolers_library_group/siTAF5L-IAA.hg19.mapq_30.1000.mcool
#POLII degron (replicates merged)
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library_group/PTB2539-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200417_remap_polIIdegron/results/coolers_library_group/PTB2539-IAA.hg19.mapq_30.1000.mcool
#CTCF degron G1 sorted to redo the insulation at a finer scale with motif search (replicates merged)
/nl/umw_job_dekker/users/av90w/distiller-run/20200805_G1sorted_442_replicate/results/coolers_library_group/G1-NT.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200805_G1sorted_442_replicate/results/coolers_library_group/G1-IAA.hg19.mapq_30.1000.mcool
# libraries to merge together to call compartments at a higher resolution (10 libraries together)
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library
CkoC44-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC44-NT-R2-T1__hg19.hg19.mapq_30.1000.mcool
CkoC44-IAA48H-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC44-IAA48H-R2-T1__hg19.hg19.mapq_30.1000.mcool
CkoC442-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC442-NT-R2-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-G1-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-NT-si-ctrl-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-NT-si-ctrl-R2-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200805_G1sorted_442_replicate/results/coolers_library
CkoCT442-G1-NT-R2-T1__hg19.hg19.mapq_30.1000.mcool
#NT libraries I forgot to add to our non treated pool:
/nl/umw_job_dekker/users/av90w/distiller-run/20201110-PDS-PlaB-rep2/results/coolers_library
CkoCT442-NT-R3-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-NT-R4-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20201119-cPDS-rep2/results/coolers_library/CkoCT442-NT-R5-T1__hg19.hg19.mapq_30.1000.mcool
#libraries to merge together for compartment IAA treated
/nl/umw_job_dekker/users/av90w/distiller-run/20200220_mapping_for_dot_calling/results/coolers_library
CkoCT442-IAA-si-ctrl-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-IAA-si-ctrl-R2-T1__hg19.hg19.mapq_30.1000.mcool
CkoC442-IAA48H-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC442-IAA48H-R2-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20200805_G1sorted_442_replicate/results/coolers_library_group/G1-IAA.hg19.mapq_30.1000.mcool
#IAA libraries I forgot to add to our IAA treated pool:
/nl/umw_job_dekker/users/av90w/distiller-run/20201110-PDS-PlaB-rep2/results/coolers_library
CkoCT442-IAA-R3-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-IAA-R4-T1__hg19.hg19.mapq_30.1000.mcool
/nl/umw_job_dekker/users/av90w/distiller-run/20201119-cPDS-rep2/results/coolers_library/CkoCT442-IAA-R5-T1__hg19.hg19.mapq_30.1000.mcool
#PDS libraries:
/nl/umw_job_dekker/users/av90w/distiller-run/20201110-PDS-PlaB-rep2/results/coolers_library
CkoCT442-NT-PDS-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-NT-PDS-R2-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-IAA-PDS-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-IAA-PDS-R2-T1__hg19.hg19.mapq_30.1000.mcool
#pooled PDS libraries
/nl/umw_job_dekker/users/av90w/distiller-run/20201110-PDS-PlaB-rep2/results/coolers_library_group
NT-PDS.hg19.mapq_30.1000.mcool
IAA-PDS.hg19.mapq_30.1000.mcool
## PlaB (splicing inhibition) two replicates pooled together
/nl/umw_job_dekker/users/av90w/cooler/20210525_PlaB_same
NT-hg19-combined-90000000.mcool
IAA-hg19-combined-90000000.mcool
NT-PlaB-hg19-combined-90000000.mcool
IAA-PlaB-hg19-combined-90000000.mcool
## RAD21-degron on HCT Rao et al 2017
/nl/umw_job_dekker/users/av90w/distiller-run/20210505_Rao_2017/results/coolers_library_group
RAD21-AID-IAA-6H.hg19.mapq_30.1000.mcool
RAD21-AID-NT.hg19.mapq_30.1000.mcool
## WAPL Haarthuis et al
/nl/umw_job_dekker/users/av90w/distiller-run/20211104_Haarthuis_WAPL/results/coolers_library
Haarthuis-HAP1-WT.hg19.mapq_30.1000.mcool
Haarthuis-WAPL-KO1.14.hg19.mapq_30.1000.mcool
Haarthuis-WAPL-KO3.3.hg19.mapq_30.1000.mcool
## compartment files
# CTCF degron non treated
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/CTCFdegron-442-nontreated-rep1.250kb.eigs.cis.vecs.txt
#AAVS1 clone
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/AAVS1sg24-nontreated.250kb.eigs.cis.vecs.txt
# DDX55sg2B clone
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/DDX55sg2B_NT-nontreated.250kb.eigs.cis.vecs.txt
## insulation files
#for asynch CTCF degron, siRNA and clones (on shadow)
/data/alv/CTCF_degron/analysis/siRNA/insulation