Annotation of ATAC (ASTARR Input) 02

Intersection (Hi-C)

Set environment

source ../run_config_project.sh
show_env

You are working on             Duke Server: RCC
BASE DIRECTORY (FD_BASE):      /data/reddylab/Kuei
REPO DIRECTORY (FD_REPO):      /data/reddylab/Kuei/repo
WORK DIRECTORY (FD_WORK):      /data/reddylab/Kuei/work
DATA DIRECTORY (FD_DATA):      /data/reddylab/Kuei/data
CONTAINER DIR. (FD_SING):      /data/reddylab/Kuei/container

You are working with           ENCODE FCC
PATH OF PROJECT (FD_PRJ):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC
PROJECT RESULTS (FD_RES):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results
PROJECT SCRIPTS (FD_EXE):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/scripts
PROJECT DATA    (FD_DAT):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data
PROJECT NOTE    (FD_NBK):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/notebooks
PROJECT DOCS    (FD_DOC):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/docs
PROJECT LOG     (FD_LOG):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/log
PROJECT REF     (FD_REF):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/references
PROJECT IMAGE   (FP_PRJ_SIF):  /data/reddylab/Kuei/container/project/singularity_proj_encode_fcc.sif
PROJECT CONF.   (FP_CNF):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/scripts/config_project.sh

Set global variables

FP_REGION_LABEL_A=${FD_RES}/region/summary/metadata.label.astarr_macs_merge.tsv
FP_REGION_LABEL_B=${FD_RES}/region/summary/metadata.label.hic.tsv

Prepare

View files

ls -1 ${FD_RES}/region

encode_chipseq_histone
encode_chipseq_subset
encode_chipseq_tf_full
encode_chromatin_states
encode_e2g_benchmark
encode_open_chromatin
fcc_astarr_csaw
fcc_astarr_macs_merge
fcc_astarr_macs_narrowpeak
fcc_crispri_growth
fcc_crispri_hcrff
fcc_screened
fcc_starrmpra_junke
fcc_table
fcc_table_cluster
genome_tss
hic_insitu_K562_ENCSR545YBD
hic_intact_K562_deep
hic_intact_K562_ENCSR479XDG
module_tf_shannon
summary
tmp

ls -1 ${FD_RES}/region/summary

metadata.label.astarr_macs_merge.tsv
metadata.label.chipseq_histone.tsv
metadata.label.chipseq_subset.tsv
metadata.label.chipseq_tf_full.tsv
metadata.label.hic.tsv
metadata.label.main.tsv
metadata.label.ocr.tsv

View: Metatable label A

ls  ${FP_REGION_LABEL_A}
cat ${FP_REGION_LABEL_A}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/summary/metadata.label.astarr_macs_merge.tsv
Folder  FName   Label   FPath
fcc_astarr_macs_merge   K562.hg38.ASTARR.macs.KS91.input.rep_all.max_overlaps.q5.bed.gz fcc_astarr_macs_input_overlap   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_merge/K562.hg38.ASTARR.macs.KS91.input.rep_all.max_overlaps.q5.bed.gz
fcc_astarr_macs_merge   K562.hg38.ASTARR.macs.KS91.input.rep_all.union.q5.bed.gz    fcc_astarr_macs_input_union /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_merge/K562.hg38.ASTARR.macs.KS91.input.rep_all.union.q5.bed.gz

cat ${FP_REGION_LABEL_A} | cut -f 1,3

Folder  Label
fcc_astarr_macs_merge   fcc_astarr_macs_input_overlap
fcc_astarr_macs_merge   fcc_astarr_macs_input_union

View: Metatable label B

ls  ${FP_REGION_LABEL_B}
cat ${FP_REGION_LABEL_B}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/summary/metadata.label.hic.tsv
Folder  FName   Label   FPath
hic_insitu_K562_ENCSR545YBD K562.hg38.hic_insitu.Loop_A.bed.gz  hic_insitu_Loop_A_ENCSR545YBD   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_insitu_K562_ENCSR545YBD/K562.hg38.hic_insitu.Loop_A.bed.gz
hic_insitu_K562_ENCSR545YBD K562.hg38.hic_insitu.Loop_B.bed.gz  hic_insitu_Loop_B_ENCSR545YBD   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_insitu_K562_ENCSR545YBD/K562.hg38.hic_insitu.Loop_B.bed.gz
hic_insitu_K562_ENCSR545YBD K562.hg38.hic_insitu.TAD.bed.gz hic_insitu_TAD_ENCSR545YBD  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_insitu_K562_ENCSR545YBD/K562.hg38.hic_insitu.TAD.bed.gz
hic_intact_K562_deep    K562.hg38.hic_intact.Loop_A.bed.gz  hic_intact_Loop_A_deep  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_deep/K562.hg38.hic_intact.Loop_A.bed.gz
hic_intact_K562_deep    K562.hg38.hic_intact.Loop_B.bed.gz  hic_intact_Loop_B_deep  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_deep/K562.hg38.hic_intact.Loop_B.bed.gz
hic_intact_K562_ENCSR479XDG K562.hg38.hic_intact.Loop_A.bed.gz  hic_intact_Loop_A_ENCSR479XDG   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_ENCSR479XDG/K562.hg38.hic_intact.Loop_A.bed.gz
hic_intact_K562_ENCSR479XDG K562.hg38.hic_intact.Loop_B.bed.gz  hic_intact_Loop_B_ENCSR479XDG   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_ENCSR479XDG/K562.hg38.hic_intact.Loop_B.bed.gz
hic_intact_K562_ENCSR479XDG K562.hg38.hic_intact.TAD.bed.gz hic_intact_TAD_ENCSR479XDG  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_ENCSR479XDG/K562.hg38.hic_intact.TAD.bed.gz

cat ${FP_REGION_LABEL_B} | cut -f 1,3

Folder  Label
hic_insitu_K562_ENCSR545YBD hic_insitu_Loop_A_ENCSR545YBD
hic_insitu_K562_ENCSR545YBD hic_insitu_Loop_B_ENCSR545YBD
hic_insitu_K562_ENCSR545YBD hic_insitu_TAD_ENCSR545YBD
hic_intact_K562_deep    hic_intact_Loop_A_deep
hic_intact_K562_deep    hic_intact_Loop_B_deep
hic_intact_K562_ENCSR479XDG hic_intact_Loop_A_ENCSR479XDG
hic_intact_K562_ENCSR479XDG hic_intact_Loop_B_ENCSR479XDG
hic_intact_K562_ENCSR479XDG hic_intact_TAD_ENCSR479XDG

Execute

Test loop

### init: set executable
FN_EXE="run_bedtools_intersect.sh"
FP_EXE=${FD_EXE}/${FN_EXE}

### init: check results and log folder
echo "- FD_RES:" ${FD_RES}
echo "- FD_LOG:" ${FD_LOG}

### Loop region A
while read FOLDER_A FNAME_A LABEL_A FPATH_A; do

    ### Set input A
    FN_INP_A=${FNAME_A}
    FP_INP_A=${FPATH_A}
    
    ### Loop region B
    while read FOLDER_B FNAME_B LABEL_B FPATH_B; do
    
        ### Set input B
        FN_INP_B=${FNAME_B}
        FP_INP_B=${FPATH_B}
        
        ### Set output
        FOLDER=region_annotation/${LABEL_A}/${FOLDER_B}
        FD_OUT=${FD_RES}/${FOLDER}
        FN_OUT=${LABEL_A}.${LABEL_B}.bed.gz
        FP_OUT=${FD_OUT}/${FN_OUT}
        
        ### setup log file
        FN_LOG=region.annotation.${LABEL_A}.${LABEL_B}.txt
        FP_LOG=${FD_LOG}/${FN_LOG}
        
        ### show progress
        echo ==============================
        echo "Input:"
        echo "- Label A:" ${LABEL_A}
        echo "- Label B:" ${LABEL_B}
        echo "Output:"
        echo "- FDiry:" '${FD_RES}'/${FOLDER}
        echo "- FName:" ${FN_OUT}
        echo "Log:" 
        echo "- FPath:" '${FD_LOG}'/${FN_LOG}
        echo  
        
    done < <(cat ${FP_REGION_LABEL_B} | head -n 3 | awk 'NR >=2 {print}')
done < <(cat ${FP_REGION_LABEL_A} | awk 'NR >=2 {print}')

- FD_RES: /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results
- FD_LOG: /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/log
==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_insitu_Loop_A_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_overlap.hic_insitu_Loop_A_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.annotation.fcc_astarr_macs_input_overlap.hic_insitu_Loop_A_ENCSR545YBD.txt

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_insitu_Loop_B_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_overlap.hic_insitu_Loop_B_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.annotation.fcc_astarr_macs_input_overlap.hic_insitu_Loop_B_ENCSR545YBD.txt

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_insitu_Loop_A_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_union.hic_insitu_Loop_A_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.annotation.fcc_astarr_macs_input_union.hic_insitu_Loop_A_ENCSR545YBD.txt

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_insitu_Loop_B_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_union.hic_insitu_Loop_B_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.annotation.fcc_astarr_macs_input_union.hic_insitu_Loop_B_ENCSR545YBD.txt

Execute

### init: set executable
FN_EXE="run_bedtools_intersect.sh"
FP_EXE=${FD_EXE}/${FN_EXE}

### init: check results and log folder
echo "- FD_RES:" ${FD_RES}
echo "- FD_LOG:" ${FD_LOG}

### Loop region A
while read FOLDER_A FNAME_A LABEL_A FPATH_A; do

    ### Set input A
    FN_INP_A=${FNAME_A}
    FP_INP_A=${FPATH_A}
    
    ### Loop region B
    while read FOLDER_B FNAME_B LABEL_B FPATH_B; do
    
        ### Set input B
        FN_INP_B=${FNAME_B}
        FP_INP_B=${FPATH_B}
        
        ### Set output
        FOLDER=region_annotation/${LABEL_A}/${FOLDER_B}
        FD_OUT=${FD_RES}/${FOLDER}
        FN_OUT=${LABEL_A}.${LABEL_B}.bed.gz
        FP_OUT=${FD_OUT}/${FN_OUT}
        
        ### setup log file
        FN_LOG=region.intersect.${LABEL_A}.${LABEL_B}.txt
        FP_LOG=${FD_LOG}/${FN_LOG}
        
        ### show progress
        echo ==============================
        echo "Input:"
        echo "- Label A:" ${LABEL_A}
        echo "- Label B:" ${LABEL_B}
        echo "Output:"
        echo "- FDiry:" '${FD_RES}'/${FOLDER}
        echo "- FName:" ${FN_OUT}
        echo "Log:" 
        echo "- FPath:" '${FD_LOG}'/${FN_LOG}
        echo  
        
        ### execute
        mkdir -p ${FD_OUT}
        sbatch \
            --cpus-per-task 4 \
            --mem 4G \
            --output ${FP_LOG} \
            ${FP_EXE} ${FP_CNF} ${FP_INP_A} ${FP_INP_B} ${FP_OUT}
        echo
    done < <(cat ${FP_REGION_LABEL_B} | awk 'NR >=2 {print}')
done < <(cat ${FP_REGION_LABEL_A} | awk 'NR >=2 {print}')

- FD_RES: /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results
- FD_LOG: /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/log
==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_insitu_Loop_A_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_overlap.hic_insitu_Loop_A_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_insitu_Loop_A_ENCSR545YBD.txt

Submitted batch job 277495

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_insitu_Loop_B_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_overlap.hic_insitu_Loop_B_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_insitu_Loop_B_ENCSR545YBD.txt

Submitted batch job 277496

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_insitu_TAD_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_overlap.hic_insitu_TAD_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_insitu_TAD_ENCSR545YBD.txt

Submitted batch job 277497

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_intact_Loop_A_deep
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_deep
- FName: fcc_astarr_macs_input_overlap.hic_intact_Loop_A_deep.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_Loop_A_deep.txt

Submitted batch job 277498

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_intact_Loop_B_deep
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_deep
- FName: fcc_astarr_macs_input_overlap.hic_intact_Loop_B_deep.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_Loop_B_deep.txt

Submitted batch job 277499

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_intact_Loop_A_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_overlap.hic_intact_Loop_A_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_Loop_A_ENCSR479XDG.txt

Submitted batch job 277500

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_intact_Loop_B_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_overlap.hic_intact_Loop_B_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_Loop_B_ENCSR479XDG.txt

Submitted batch job 277501

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: hic_intact_TAD_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_overlap.hic_intact_TAD_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_TAD_ENCSR479XDG.txt

Submitted batch job 277502

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_insitu_Loop_A_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_union.hic_insitu_Loop_A_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_insitu_Loop_A_ENCSR545YBD.txt

Submitted batch job 277503

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_insitu_Loop_B_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_union.hic_insitu_Loop_B_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_insitu_Loop_B_ENCSR545YBD.txt

Submitted batch job 277504

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_insitu_TAD_ENCSR545YBD
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_insitu_K562_ENCSR545YBD
- FName: fcc_astarr_macs_input_union.hic_insitu_TAD_ENCSR545YBD.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_insitu_TAD_ENCSR545YBD.txt

Submitted batch job 277505

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_intact_Loop_A_deep
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_deep
- FName: fcc_astarr_macs_input_union.hic_intact_Loop_A_deep.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_Loop_A_deep.txt

Submitted batch job 277506

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_intact_Loop_B_deep
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_deep
- FName: fcc_astarr_macs_input_union.hic_intact_Loop_B_deep.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_Loop_B_deep.txt

Submitted batch job 277507

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_intact_Loop_A_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_union.hic_intact_Loop_A_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_Loop_A_ENCSR479XDG.txt

Submitted batch job 277508

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_intact_Loop_B_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_union.hic_intact_Loop_B_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_Loop_B_ENCSR479XDG.txt

Submitted batch job 277509

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: hic_intact_TAD_ENCSR479XDG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_ENCSR479XDG
- FName: fcc_astarr_macs_input_union.hic_intact_TAD_ENCSR479XDG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_TAD_ENCSR479XDG.txt

Submitted batch job 277510

Review

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_TAD_ENCSR479XDG.txt

Hostname:           plp-rcc-node-05
Slurm Array Index: 
Time Stamp:         05-29-25+16:40:04

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_merge/K562.hg38.ASTARR.macs.KS91.input.rep_all.union.q5.bed.gz

show first few lines of input
chr1    10015   10442   chr1:10015-10442
chr1    14253   14645   chr1:14253-14645
chr1    16015   16477   chr1:16015-16477
chr1    17237   17772   chr1:17237-17772
chr1    28903   29613   chr1:28903-29613
chr1    30803   31072   chr1:30803-31072
chr1    101603  101849  chr1:101603-101849
chr1    115411  115986  chr1:115411-115986
chr1    118518  118743  chr1:118518-118743
chr1    136071  137429  chr1:136071-137429

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_ENCSR479XDG/K562.hg38.hic_intact.TAD.bed.gz

show first few lines of input
chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD
chr1    1940000 2040000 chr1:1940000-2040000    hic_intact  TAD
chr1    2205000 2310000 chr1:2205000-2310000    hic_intact  TAD
chr1    2410000 2525000 chr1:2410000-2525000    hic_intact  TAD
chr1    2820000 3430000 chr1:2820000-3430000    hic_intact  TAD
chr1    3490000 3620000 chr1:3490000-3620000    hic_intact  TAD
chr1    6040000 6205000 chr1:6040000-6205000    hic_intact  TAD
chr1    6245000 6340000 chr1:6245000-6340000    hic_intact  TAD
chr1    6550000 6645000 chr1:6550000-6645000    hic_intact  TAD
chr1    6710000 6785000 chr1:6710000-6785000    hic_intact  TAD


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_ENCSR479XDG/fcc_astarr_macs_input_union.hic_intact_TAD_ENCSR479XDG.bed.gz

show first few lines of output:
chr1    1121788 1122529 chr1:1121788-1122529    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 741
chr1    1122893 1123442 chr1:1122893-1123442    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 549
chr1    1124347 1125709 chr1:1124347-1125709    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1362
chr1    1127455 1129027 chr1:1127455-1129027    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1572
chr1    1134673 1136326 chr1:1134673-1136326    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1653
chr1    1136833 1138125 chr1:1136833-1138125    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1292
chr1    1141732 1143168 chr1:1141732-1143168    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1436
chr1    1143425 1143844 chr1:1143425-1143844    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 419
chr1    1144125 1145439 chr1:1144125-1145439    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 1314
chr1    1148300 1148832 chr1:1148300-1148832    chr1    1120000 1240000 chr1:1120000-1240000    hic_intact  TAD 532


Done!
Run Time: 1 seconds

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.hic_intact_Loop_B_deep.txt

Hostname:           plp-rcc-node-05
Slurm Array Index: 
Time Stamp:         05-29-25+16:40:04

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_merge/K562.hg38.ASTARR.macs.KS91.input.rep_all.union.q5.bed.gz

show first few lines of input
chr1    10015   10442   chr1:10015-10442
chr1    14253   14645   chr1:14253-14645
chr1    16015   16477   chr1:16015-16477
chr1    17237   17772   chr1:17237-17772
chr1    28903   29613   chr1:28903-29613
chr1    30803   31072   chr1:30803-31072
chr1    101603  101849  chr1:101603-101849
chr1    115411  115986  chr1:115411-115986
chr1    118518  118743  chr1:118518-118743
chr1    136071  137429  chr1:136071-137429

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_deep/K562.hg38.hic_intact.Loop_B.bed.gz

show first few lines of input
chr1    827000  828000  chr1:778000-779000|chr1:827000-828000   hic_intact  Loop_B
chr1    923000  924000  chr1:906000-907000|chr1:923000-924000   hic_intact  Loop_B
chr1    935000  940000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_B
chr1    940000  941000  chr1:925000-926000|chr1:940000-941000   hic_intact  Loop_B
chr1    940000  941000  chr1:904000-905000|chr1:940000-941000   hic_intact  Loop_B
chr1    959000  960000  chr1:940000-941000|chr1:959000-960000   hic_intact  Loop_B
chr1    959000  960000  chr1:906000-907000|chr1:959000-960000   hic_intact  Loop_B
chr1    959000  960000  chr1:921000-922000|chr1:959000-960000   hic_intact  Loop_B
chr1    966000  968000  chr1:904000-906000|chr1:966000-968000   hic_intact  Loop_B
chr1    974000  976000  chr1:870000-872000|chr1:974000-976000   hic_intact  Loop_B


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_union/hic_intact_K562_deep/fcc_astarr_macs_input_union.hic_intact_Loop_B_deep.bed.gz

show first few lines of output:
chr1    826754  828040  chr1:826754-828040  chr1    827000  828000  chr1:778000-779000|chr1:827000-828000   hic_intact  Loop_B  1000
chr1    923417  925194  chr1:923417-925194  chr1    923000  924000  chr1:906000-907000|chr1:923000-924000   hic_intact  Loop_B  583
chr1    935605  936252  chr1:935605-936252  chr1    935000  940000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_B  647
chr1    938228  938505  chr1:938228-938505  chr1    935000  940000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_B  277
chr1    939127  939463  chr1:939127-939463  chr1    935000  940000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_B  336
chr1    940325  943460  chr1:940325-943460  chr1    940000  941000  chr1:925000-926000|chr1:940000-941000   hic_intact  Loop_B  675
chr1    940325  943460  chr1:940325-943460  chr1    940000  941000  chr1:904000-905000|chr1:940000-941000   hic_intact  Loop_B  675
chr1    958685  959974  chr1:958685-959974  chr1    959000  960000  chr1:940000-941000|chr1:959000-960000   hic_intact  Loop_B  974
chr1    958685  959974  chr1:958685-959974  chr1    959000  960000  chr1:906000-907000|chr1:959000-960000   hic_intact  Loop_B  974
chr1    958685  959974  chr1:958685-959974  chr1    959000  960000  chr1:921000-922000|chr1:959000-960000   hic_intact  Loop_B  974


Done!
Run Time: 1 seconds

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.hic_intact_Loop_A_deep.txt

Hostname:           plp-rcc-node-03
Slurm Array Index: 
Time Stamp:         05-29-25+16:40:04

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_merge/K562.hg38.ASTARR.macs.KS91.input.rep_all.max_overlaps.q5.bed.gz

show first few lines of input
chr1    10038   10405   chr1:10038-10405
chr1    14282   14614   chr1:14282-14614
chr1    16025   16338   chr1:16025-16338
chr1    17288   17689   chr1:17288-17689
chr1    28934   29499   chr1:28934-29499
chr1    115429  115969  chr1:115429-115969
chr1    136201  137353  chr1:136201-137353
chr1    137748  138049  chr1:137748-138049
chr1    138321  139517  chr1:138321-139517
chr1    181005  181854  chr1:181005-181854

Input:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/hic_intact_K562_deep/K562.hg38.hic_intact.Loop_A.bed.gz

show first few lines of input
chr1    778000  779000  chr1:778000-779000|chr1:827000-828000   hic_intact  Loop_A
chr1    868000  870000  chr1:868000-870000|chr1:1290000-1292000 hic_intact  Loop_A
chr1    870000  872000  chr1:870000-872000|chr1:974000-976000   hic_intact  Loop_A
chr1    870000  872000  chr1:870000-872000|chr1:1062000-1064000 hic_intact  Loop_A
chr1    870000  875000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_A
chr1    904000  905000  chr1:904000-905000|chr1:976000-977000   hic_intact  Loop_A
chr1    904000  905000  chr1:904000-905000|chr1:1062000-1063000 hic_intact  Loop_A
chr1    904000  905000  chr1:904000-905000|chr1:940000-941000   hic_intact  Loop_A
chr1    904000  905000  chr1:904000-905000|chr1:1000000-1001000 hic_intact  Loop_A
chr1    904000  906000  chr1:904000-906000|chr1:966000-968000   hic_intact  Loop_A


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_overlap/hic_intact_K562_deep/fcc_astarr_macs_input_overlap.hic_intact_Loop_A_deep.bed.gz

show first few lines of output:
chr1    778233  779389  chr1:778233-779389  chr1    778000  779000  chr1:778000-779000|chr1:827000-828000   hic_intact  Loop_A  767
chr1    869637  870233  chr1:869637-870233  chr1    870000  872000  chr1:870000-872000|chr1:974000-976000   hic_intact  Loop_A  233
chr1    869637  870233  chr1:869637-870233  chr1    870000  872000  chr1:870000-872000|chr1:1062000-1064000 hic_intact  Loop_A  233
chr1    869637  870233  chr1:869637-870233  chr1    870000  875000  chr1:870000-875000|chr1:935000-940000   hic_intact  Loop_A  233
chr1    869637  870233  chr1:869637-870233  chr1    868000  870000  chr1:868000-870000|chr1:1290000-1292000 hic_intact  Loop_A  363
chr1    903783  905204  chr1:903783-905204  chr1    904000  905000  chr1:904000-905000|chr1:976000-977000   hic_intact  Loop_A  1000
chr1    903783  905204  chr1:903783-905204  chr1    904000  905000  chr1:904000-905000|chr1:1062000-1063000 hic_intact  Loop_A  1000
chr1    903783  905204  chr1:903783-905204  chr1    904000  905000  chr1:904000-905000|chr1:940000-941000   hic_intact  Loop_A  1000
chr1    903783  905204  chr1:903783-905204  chr1    904000  905000  chr1:904000-905000|chr1:1000000-1001000 hic_intact  Loop_A  1000
chr1    903783  905204  chr1:903783-905204  chr1    904000  906000  chr1:904000-906000|chr1:966000-968000   hic_intact  Loop_A  1204


Done!
Run Time: 1 seconds