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README-ChIP-seq.txt
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README-ChIP-seq.txt
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## ChIP seq bigwig
#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
## 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
# Locations of the files for DDX55 for fig4:
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01
NT-CTCF-narrowPeak-withDDX55-centered-CTCF
NT-CTCF-narrowPeak-noDDX55-centered-CTCF
NT-DDX55-narrowPeak-noCTCF-centered-DDX55
IAA-CTCF-narrowPeak-withDDX55-centered-CTCF
IAA-CTCF-narrowPeak-noDDX55-centered-CTCF
IAA-DDX55-narrowPeak-noCTCF-centered-DDX55
# Locations of the files for TAF5L for fig4:
/nl/umw_job_dekker/users/av90w/ChIPseq/ChIP4/MACS2/narrow0.01
NT-CTCF-narrowPeak-withTAF5L-centered-CTCF
NT-CTCF-narrowPeak-noTAF5L-centered-CTCF
NT-TAF5L-narrowPeak-noCTCF-centered-TAF5L
IAA-CTCF-narrowPeak-withTAF5L-centered-CTCF
IAA-CTCF-narrowPeak-noTAF5L-centered-CTCF
IAA-TAF5L-narrowPeak-noCTCF-centered-TAF5L
# 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
## RNA seq
/nl/umw_job_dekker/users/av90w/RNAseq/data/siRNA/report2546/bigwig_star/S442_NT.bw
/nl/umw_job_dekker/users/av90w/RNAseq/data/siRNA/report2546/bigwig_star/S442_NTR2.bw
#RSEM for siRNA (and 44 and 442)
/nl/umw_job_dekker/users/av90w/RNAseq/data/siRNA/report2546/rsem/mergedRSEM/merged_TPM_genes.tsv
#RSEM for clones (and 44 and 442)
/nl/umw_job_dekker/users/av90w/RNAseq/data/siRNA/report2547/rsem/mergedRSEM/merged_TPM_genes.tsv
## 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