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README.txt
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##What do we miss for the paper?
R-loop boundaries NO CTCF NO G4 do not show cohesin accumulation. Are they compartment boundaries? or are they boundaries that do not show RAD21 accumulation?
## to do heatmap style to represent the DEAD box helicases in the screen
/nl/umw_job_dekker/users/av90w/projects/for-paper/stem/FC_T6_DEADboxhelicases
/nl/umw_job_dekker/users/av90w/projects/for-paper/stem/FC_T15_DEADboxhelicases
## BED File locations
# The different categories used in the paper
# R-loops NO CTCF G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-Rloops-NO-all-NT-CTCF-G4-Mao
R-loops NO CTCF NO G4 (####### THIS IS THE CATEGORY WE WOULD KNOW IF THEY ARE COMPARTMENTS BOUNDARIES)
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-Rloops-NO-all-NT-CTCF-NO-G4-Mao
CTCF NO R-loops G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-all-NT-CTCF-NO-Rloops-G4-Mao
CTCF NO R-loops NO G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-all-NT-CTCF-NO-Rloops-NO-G4-Mao
CTCF R-loops G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-all-NT-CTCF-Rloops-G4-Mao
CTCF R-loops NO G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/diff-cat/intersect-all-NT-CTCF-Rloops-NO-G4-Mao
# ALL R-loops
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/GSM1720619_K562_DRIP_peaks-sort.bed
# G4 different categories
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/deeptools/G4/mao/intersect-G4-NO-CTCF
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/deeptools/G4/mao/intersect-all-NT-CTCF-G4
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/deeptools/G4/mao/intersect-all-NT-CTCF-NO-G4
# G4 different categories CENTERED on peaks
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/deeptools/G4/mao/recenter/
intersect-all-NT-CTCF-G4-centered
intersect-all-NT-CTCF-NO-G4-centered
intersect-G4-NO-CTCF-centered
# ALL G4
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/G4-Mao-sort
#for Fig4
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/deeptools/
NT-CTCF-narrowPeak-noDDX55
NT-CTCF-narrowPeak-withDDX55
NT-DDX55-narrowPeak-noCTCF
IAA-CTCF-narrowPeak-noDDX55
IAA-CTCF-narrowPeak-withDDX55
IAA-DDX55-narrowPeak-noCTCF
# ChIP seq peaks
CTCF peaks
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/NT-CTCF-narrowPeaks-sort-merge-with-strength.bed
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/IAA-CTCF-narrowPeaks-sort-merge-with-strength.bed
DDX55 peaks
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/NT-DDX55-narrowPeaks-sort-merge-with-strength.bed
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/IAA-DDX55-narrowPeaks-sort-merge-with-strength.bed
RAD21 peaks
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/NT-RAD21-narrowPeaks-sort-merge-with-strength.bed
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/IAA-RAD21-narrowPeaks-sort-merge-with-strength.bed
TAF5L peaks
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/NT-TAF5L-narrowPeaks-sort-merge-with-strength.bed
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01/IAA-TAF5L-narrowPeaks-sort-merge-with-strength.bed
# splicing events
# In CTCF degron after CTCF depletion
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/S44_NT_S442_IAA.output_events_all_select_hg19.txt
# In DDX55 clone1
/nl/umw_job_dekker/users/av90w/projects/for-paper/for-higlass/AAVS1_sg24_NT_DDX55_sg2B_NT.output_events_all_select_hg19.txt
## 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
# 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
#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
## 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
## ChIP seq
#RAD21 bigwig
rep1
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/NT-RAD21_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/IAA-RAD21_R1.mLb.clN.bigWig
rep2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP4-bis/results/bwa/mergedLibrary/bigwig/NT-RAD21_R2.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/IAA-RAD21_R1.mLb.clN.bigWig
#CTCF bigWig
rep1
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/NT-CTCF_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/IAA-CTCF_R1.mLb.clN.bigWig
rep2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP4-bis/results/bwa/mergedLibrary/bigwig/NT-CTCF_R2.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP4-bis/results/bwa/mergedLibrary/bigwig/IAA-CTCF_R2.mLb.clN.bigWig
#DDX55 bigWig
rep1
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/NT-DDX55_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/IAA-DDX55_R1.mLb.clN.bigWig
rep2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/NT-DDX55_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/IAA-DDX55_R1.mLb.clN.bigWig
#TAF5L bigWig
rep1
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/NT-TAF5L_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/IAA-TAF5L_R1.mLb.clN.bigWig
rep2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/NT-TAF5L_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/IAA-TAF5L_R1.mLb.clN.bigWig
#input control bigwig
#input controls for IAA RAD21 R2, CTCF R1, DDX55 R2, TAF5L R2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/NT-input_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP3/results/bwa/mergedLibrary/bigwig/IAA-input_R1.mLb.clN.bigWig
#input controls for NT RAD21 R2, CTCF R2
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP4-bis/results/bwa/mergedLibrary/bigwig/NT-input_R2.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/ChIP4-bis/results/bwa/mergedLibrary/bigwig/IAA-input_R2.mLb.clN.bigWig
#input controls for RAD21 R1, DDX55 R1, TAF5L R1
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/NT-input_R1.mLb.clN.bigWig
/nl/umw_job_dekker/users/av90w/ChIPseq/fastq/test-ChIP2/new-mapping/results/bwa/mergedLibrary/bigwig/IAA-input_R1.mLb.clN.bigWig
#K562 G4 ChIP-seq bigwig
#to download for eg: wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1720nnn/GSM1720619/suppl/GSM1720619_K562_DRIP_peaks.bed.gz
GSM2876090_B_REP1.SLX-12319.K562_asynch_a_701_504.clean.bw
GSM2876091_B_REP1.SLX-12319.K562_asynch_c_703_504.clean.bw
GSM2876093_B_REP2.SLX-12320.K562_P9_Async_c_701_503.rmdup.clean.bw
GSM2876094_B_REP2.SLX-12320.K562_P9_Async_b_701_502.rmdup.clean.bw
GSM2876095_B_REP2.SLX-12320.K562_P9_Async_a_701_517.rmdup.clean.bw
## RNA seq
/nl/umw_job_dekker/users/av90w/RNAseq/data/siRNA/report2546/bigwig_star/S442_NT.bw