Annotation of ATAC (ASTARR Input) 01

Intersection (Main)

Set environment

Code

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

Code

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

Prepare

View files

Code

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_cres
genome_tss
hic_insitu_K562_ENCSR545YBD
hic_intact_K562_deep
hic_intact_K562_ENCSR479XDG
module_tf_shannon
region_for_analysis
summary
tmp

Code

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
metadata.label.region_for_analysis.tsv

View: Metatable label A

Code

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

Code

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

Code

ls  ${FP_REGION_LABEL_B}
cat ${FP_REGION_LABEL_B}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/summary/metadata.label.main.tsv
Folder  FName   Label   FPath
encode_chromatin_states K562.hg38.cCREs.silencer_rest.bed.gz    encode_ccres_silencer_rest  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/encode_chromatin_states/K562.hg38.cCREs.silencer_rest.bed.gz
encode_chromatin_states K562.hg38.cCREs.silencer_starr.bed.gz   encode_ccres_silencer_starr /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/encode_chromatin_states/K562.hg38.cCREs.silencer_starr.bed.gz
encode_chromatin_states K562.hg38.ENCSR365YNI.ENCFF106BGJ.ChromHMM.simplified.bed.gz    encode_chromhmm_ENCFF106BGJ /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/encode_chromatin_states/K562.hg38.ENCSR365YNI.ENCFF106BGJ.ChromHMM.simplified.bed.gz
encode_chromatin_states K562.hg38.ENCSR913HQX.ENCFF286VQG.cCREs.simplified.bed.gz   encode_ccres_ENCFF286VQG    /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/encode_chromatin_states/K562.hg38.ENCSR913HQX.ENCFF286VQG.cCREs.simplified.bed.gz
encode_e2g_benchmark    K562.hg38.ENCODE_E2G.benchmark.bed.gz   encode_e2g_benchmark    /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/encode_e2g_benchmark/K562.hg38.ENCODE_E2G.benchmark.bed.gz
fcc_astarr_csaw K562.hg38.ASTARR.csaw.KS91.bed.gz   fcc_astarr_csaw_KS91    /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_csaw/K562.hg38.ASTARR.csaw.KS91.bed.gz
fcc_astarr_csaw K562.hg38.ASTARR.csaw.KSMerge.bed.gz    fcc_astarr_csaw_KSMerge /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_csaw/K562.hg38.ASTARR.csaw.KSMerge.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep1.narrowpeak.bed.gz fcc_astarr_macs_input_rep1  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep1.narrowpeak.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep2.narrowpeak.bed.gz fcc_astarr_macs_input_rep2  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep2.narrowpeak.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep3.narrowpeak.bed.gz fcc_astarr_macs_input_rep3  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep3.narrowpeak.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep4.narrowpeak.bed.gz fcc_astarr_macs_input_rep4  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep4.narrowpeak.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep5.narrowpeak.bed.gz fcc_astarr_macs_input_rep5  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep5.narrowpeak.bed.gz
fcc_astarr_macs_narrowpeak  K562.hg38.ASTARR.macs.KS91.Input.rep6.narrowpeak.bed.gz fcc_astarr_macs_input_rep6  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep6.narrowpeak.bed.gz
fcc_crispri_growth  K562.hg38.CRISPRi_Growth.signif.bed.gz  fcc_crispri_growth_signif   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_crispri_growth/K562.hg38.CRISPRi_Growth.signif.bed.gz
fcc_crispri_growth  K562.hg38.CRISPRi_Growth.total.bed.gz   fcc_crispri_growth_total    /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_crispri_growth/K562.hg38.CRISPRi_Growth.total.bed.gz
fcc_crispri_hcrff   K562.hg38.CRISPRi_HCRFF.CASA.bed.gz fcc_crispri_hcrff_casa  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_crispri_hcrff/K562.hg38.CRISPRi_HCRFF.CASA.bed.gz
fcc_starrmpra_junke K562.hg38.ASTARR.junke.bed.gz   fcc_starrmpra_junke_astarr  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_starrmpra_junke/K562.hg38.ASTARR.junke.bed.gz
fcc_starrmpra_junke K562.hg38.eSTARR.junke.bed.gz   fcc_starrmpra_junke_estarr  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_starrmpra_junke/K562.hg38.eSTARR.junke.bed.gz
fcc_starrmpra_junke K562.hg38.LMPRA.junke.bed.gz    fcc_starrmpra_junke_lmpra   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_starrmpra_junke/K562.hg38.LMPRA.junke.bed.gz
fcc_starrmpra_junke K562.hg38.TMPRA.junke.bed.gz    fcc_starrmpra_junke_tmpra   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_starrmpra_junke/K562.hg38.TMPRA.junke.bed.gz
fcc_starrmpra_junke K562.hg38.WSTARR.junke.bed.gz   fcc_starrmpra_junke_wstarr  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_starrmpra_junke/K562.hg38.WSTARR.junke.bed.gz
genome_cres K562.hg38.label_cres.bed.gz genome_cres /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/genome_cres/K562.hg38.label_cres.bed.gz
genome_tss  K562.hg38.TSS.selected_by_highest_Pol2_signal.bed.gz    genome_tss_pol2 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/genome_tss/K562.hg38.TSS.selected_by_highest_Pol2_signal.bed.gz
genome_tss  K562.hg38.TSS.selected_by_highest_Pol2_signal.filtered_by_RNAseq_TPM.bed.gz genome_tss_pol2_rnaseq  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/genome_tss/K562.hg38.TSS.selected_by_highest_Pol2_signal.filtered_by_RNAseq_TPM.bed.gz
module_tf_shannon   K562.hg38.TF_Module.bed.gz  module_tf_shannon   /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/module_tf_shannon/K562.hg38.TF_Module.bed.gz

Code

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

Folder  Label
encode_chromatin_states encode_ccres_silencer_rest
encode_chromatin_states encode_ccres_silencer_starr
encode_chromatin_states encode_chromhmm_ENCFF106BGJ
encode_chromatin_states encode_ccres_ENCFF286VQG
encode_e2g_benchmark    encode_e2g_benchmark
fcc_astarr_csaw fcc_astarr_csaw_KS91
fcc_astarr_csaw fcc_astarr_csaw_KSMerge
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep1
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep2
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep3
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep4
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep5
fcc_astarr_macs_narrowpeak  fcc_astarr_macs_input_rep6
fcc_crispri_growth  fcc_crispri_growth_signif
fcc_crispri_growth  fcc_crispri_growth_total
fcc_crispri_hcrff   fcc_crispri_hcrff_casa
fcc_starrmpra_junke fcc_starrmpra_junke_astarr
fcc_starrmpra_junke fcc_starrmpra_junke_estarr
fcc_starrmpra_junke fcc_starrmpra_junke_lmpra
fcc_starrmpra_junke fcc_starrmpra_junke_tmpra
fcc_starrmpra_junke fcc_starrmpra_junke_wstarr
genome_cres genome_cres
genome_tss  genome_tss_pol2
genome_tss  genome_tss_pol2_rnaseq
module_tf_shannon   module_tf_shannon

Execute

Test loop

Code

### 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: encode_ccres_silencer_rest
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/encode_chromatin_states
- FName: fcc_astarr_macs_input_overlap.encode_ccres_silencer_rest.bed.gz
Log:
- FPath: ${FD_LOG}/region.annotation.fcc_astarr_macs_input_overlap.encode_ccres_silencer_rest.txt

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

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

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

Execute

Code

### 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: encode_ccres_silencer_rest
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/encode_chromatin_states
- FName: fcc_astarr_macs_input_overlap.encode_ccres_silencer_rest.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.encode_ccres_silencer_rest.txt

Submitted batch job 305978

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

Submitted batch job 305979

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: encode_chromhmm_ENCFF106BGJ
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/encode_chromatin_states
- FName: fcc_astarr_macs_input_overlap.encode_chromhmm_ENCFF106BGJ.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.encode_chromhmm_ENCFF106BGJ.txt

Submitted batch job 305980

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: encode_ccres_ENCFF286VQG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/encode_chromatin_states
- FName: fcc_astarr_macs_input_overlap.encode_ccres_ENCFF286VQG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.encode_ccres_ENCFF286VQG.txt

Submitted batch job 305981

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: encode_e2g_benchmark
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/encode_e2g_benchmark
- FName: fcc_astarr_macs_input_overlap.encode_e2g_benchmark.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.encode_e2g_benchmark.txt

Submitted batch job 305982

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_csaw_KS91
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_csaw
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_csaw_KS91.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_csaw_KS91.txt

Submitted batch job 305983

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

Submitted batch job 305984

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep1
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep1.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep1.txt

Submitted batch job 305985

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep2
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep2.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep2.txt

Submitted batch job 305986

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep3
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep3.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep3.txt

Submitted batch job 305987

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep4
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep4.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep4.txt

Submitted batch job 305988

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep5
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep5.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep5.txt

Submitted batch job 305989

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: fcc_astarr_macs_input_rep6
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep6.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.fcc_astarr_macs_input_rep6.txt

Submitted batch job 305990

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

Submitted batch job 305991

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

Submitted batch job 305992

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

Submitted batch job 305993

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

Submitted batch job 305994

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

Submitted batch job 305995

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

Submitted batch job 305996

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

Submitted batch job 305997

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

Submitted batch job 305998

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

Submitted batch job 305999

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: genome_tss_pol2
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/genome_tss
- FName: fcc_astarr_macs_input_overlap.genome_tss_pol2.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.genome_tss_pol2.txt

Submitted batch job 306000

==============================
Input:
- Label A: fcc_astarr_macs_input_overlap
- Label B: genome_tss_pol2_rnaseq
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_overlap/genome_tss
- FName: fcc_astarr_macs_input_overlap.genome_tss_pol2_rnaseq.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.genome_tss_pol2_rnaseq.txt

Submitted batch job 306001

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

Submitted batch job 306002

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

Submitted batch job 306003

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

Submitted batch job 306004

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: encode_chromhmm_ENCFF106BGJ
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/encode_chromatin_states
- FName: fcc_astarr_macs_input_union.encode_chromhmm_ENCFF106BGJ.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.encode_chromhmm_ENCFF106BGJ.txt

Submitted batch job 306005

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: encode_ccres_ENCFF286VQG
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/encode_chromatin_states
- FName: fcc_astarr_macs_input_union.encode_ccres_ENCFF286VQG.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.encode_ccres_ENCFF286VQG.txt

Submitted batch job 306006

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: encode_e2g_benchmark
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/encode_e2g_benchmark
- FName: fcc_astarr_macs_input_union.encode_e2g_benchmark.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.encode_e2g_benchmark.txt

Submitted batch job 306007

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_csaw_KS91
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_csaw
- FName: fcc_astarr_macs_input_union.fcc_astarr_csaw_KS91.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_csaw_KS91.txt

Submitted batch job 306008

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

Submitted batch job 306009

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep1
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep1.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep1.txt

Submitted batch job 306010

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep2
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep2.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep2.txt

Submitted batch job 306011

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep3
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep3.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep3.txt

Submitted batch job 306012

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep4
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep4.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep4.txt

Submitted batch job 306013

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep5
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep5.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep5.txt

Submitted batch job 306014

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: fcc_astarr_macs_input_rep6
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak
- FName: fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep6.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep6.txt

Submitted batch job 306015

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

Submitted batch job 306016

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

Submitted batch job 306017

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

Submitted batch job 306018

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

Submitted batch job 306019

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

Submitted batch job 306020

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

Submitted batch job 306021

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

Submitted batch job 306022

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

Submitted batch job 306023

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

Submitted batch job 306024

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: genome_tss_pol2
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/genome_tss
- FName: fcc_astarr_macs_input_union.genome_tss_pol2.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.genome_tss_pol2.txt

Submitted batch job 306025

==============================
Input:
- Label A: fcc_astarr_macs_input_union
- Label B: genome_tss_pol2_rnaseq
Output:
- FDiry: ${FD_RES}/region_annotation/fcc_astarr_macs_input_union/genome_tss
- FName: fcc_astarr_macs_input_union.genome_tss_pol2_rnaseq.bed.gz
Log:
- FPath: ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.genome_tss_pol2_rnaseq.txt

Submitted batch job 306026

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

Submitted batch job 306027

Review

Code

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.encode_e2g_benchmark.txt

Hostname:           plp-rcc-node-02
Slurm Array Index: 
Time Stamp:         07-21-25+16:03:00

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/encode_e2g_benchmark/K562.hg38.ENCODE_E2G.benchmark.bed.gz

show first few lines of input
chr1    3774714 3775214 CEP104|chr1:3691278-3691778:*   -0.293431866    -4.705144009935936  chr1:3774714-3775214    CEP104  2.3953437547725875  TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE
chr1    3774714 3775214 LRRC47|chr1:3691278-3691778:*   -0.331178093    -5.331209058740296  chr1:3774714-3775214    LRRC47  2.109513702198715   TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE
chr1    3774714 3775214 SMIM1|chr1:3691278-3691778:*    -0.472019217    -7.66722280577575   chr1:3774714-3775214    SMIM1   3.1927024782384743  TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE
chr1    3803570 3805848 LRRC47|chr1:3720134-3722412:.   -0.00147126515217055    0.13736191307317389 chr1:3803570-3805848    LRRC47  3.542646476960444e-5    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE
chr1    3803570 3805848 SMIM1|chr1:3720134-3722412:.    0.02567692399390253 0.5876461855300268  chr1:3803570-3805848    SMIM1   0.002543853964790131    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE
chr1    4126791 4127291 SMIM1|chr1:4186851-4187351:.    0.02338378715953637 0.5496118457237589  chr1:4126791-4127291    SMIM1   0.0034020324885204794   FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE
chr1    5304578 5305078 RPL22|chr1:5364638-5365138:.    0.02672188376700024 0.6049780579670524  chr1:5304578-5305078    RPL22   0.004330207730075751    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE
chr1    8197448 8198244 PARK7|chr1:8257508-8258304:.    -0.01987717740799877    -0.16792153564698162    chr1:8197448-8198244    PARK7   0.019584924569034646    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE
chr1    8858063 8858563 ENO1|chr1:8918122-8918622:. -0.10740945598182072    -1.6197461182013284 chr1:8858063-8858563    ENO1    2.356934408285695   TRUE    Gasperini et al., 2019  E2G-Benchmark   Regulated:TRUE
chr1    8899850 8900350 PARK7|chr1:8959909-8960409:.    -0.0418823955064419 -0.5329036553897673 chr1:8899850-8900350    PARK7   0.01789484066353039 FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_overlap/encode_e2g_benchmark/fcc_astarr_macs_input_overlap.encode_e2g_benchmark.bed.gz

show first few lines of output:
chr1    3774056 3776283 chr1:3774056-3776283    chr1    3774714 3775214 CEP104|chr1:3691278-3691778:*   -0.293431866    -4.705144009935936  chr1:3774714-3775214    CEP104  2.3953437547725875  TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE  500
chr1    3774056 3776283 chr1:3774056-3776283    chr1    3774714 3775214 LRRC47|chr1:3691278-3691778:*   -0.331178093    -5.331209058740296  chr1:3774714-3775214    LRRC47  2.109513702198715   TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE  500
chr1    3774056 3776283 chr1:3774056-3776283    chr1    3774714 3775214 SMIM1|chr1:3691278-3691778:*    -0.472019217    -7.66722280577575   chr1:3774714-3775214    SMIM1   3.1927024782384743  TRUE    Ulirsch2016 E2G-Benchmark   Regulated:TRUE  500
chr1    3803955 3806146 chr1:3803955-3806146    chr1    3803570 3805848 LRRC47|chr1:3720134-3722412:.   -0.00147126515217055    0.13736191307317389 chr1:3803570-3805848    LRRC47  3.542646476960444e-5    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 1893
chr1    3803955 3806146 chr1:3803955-3806146    chr1    3803570 3805848 SMIM1|chr1:3720134-3722412:.    0.02567692399390253 0.5876461855300268  chr1:3803570-3805848    SMIM1   0.002543853964790131    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 1893
chr1    4126841 4128109 chr1:4126841-4128109    chr1    4126791 4127291 SMIM1|chr1:4186851-4187351:.    0.02338378715953637 0.5496118457237589  chr1:4126791-4127291    SMIM1   0.0034020324885204794   FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 450
chr1    5304733 5305546 chr1:5304733-5305546    chr1    5304578 5305078 RPL22|chr1:5364638-5365138:.    0.02672188376700024 0.6049780579670524  chr1:5304578-5305078    RPL22   0.004330207730075751    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 345
chr1    8197576 8198589 chr1:8197576-8198589    chr1    8197448 8198244 PARK7|chr1:8257508-8258304:.    -0.01987717740799877    -0.16792153564698162    chr1:8197448-8198244    PARK7   0.019584924569034646    FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 668
chr1    8857787 8858608 chr1:8857787-8858608    chr1    8858063 8858563 ENO1|chr1:8918122-8918622:. -0.10740945598182072    -1.6197461182013284 chr1:8858063-8858563    ENO1    2.356934408285695   TRUE    Gasperini et al., 2019  E2G-Benchmark   Regulated:TRUE  500
chr1    8899651 8900948 chr1:8899651-8900948    chr1    8899850 8900350 PARK7|chr1:8959909-8960409:.    -0.0418823955064419 -0.5329036553897673 chr1:8899850-8900350    PARK7   0.01789484066353039 FALSE   Gasperini et al., 2019  E2G-Benchmark   Regulated:FALSE 500


Done!
Run Time: 4 seconds

Code

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_csaw_KS91.txt

Hostname:           plp-rcc-node-20
Slurm Array Index: 
Time Stamp:         07-21-25+16:03:04

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/fcc_astarr_csaw/K562.hg38.ASTARR.csaw.KS91.bed.gz

show first few lines of input
chr1    9976    10475   chr1:9976-10475 62  .   -4.184  0.204   0.002   7.358   6.299   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    14226   14675   chr1:14226-14675    79  .   -6.187  0.209   0   9.192   7.917   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    15976   16525   chr1:15976-16525    42  .   -2.236  0.196   0.013   5.062   4.267   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    17201   17800   chr1:17201-17800    64  .   -1.944  0.79    0.021   7.506   6.429   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    28876   29650   chr1:28876-29650    76  .   -2.559  0.691   0.016   8.94    7.698   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    30776   31100   chr1:30776-31100    40  .   -2.501  0.252   0.003   4.826   4.06    KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    101576  101875  chr1:101576-101875  14  .   -0.908  0.113   0.011   1.736   1.419   KS91    ASTARR  ASTARR_R:csaw:KS91
chr1    115376  115975  chr1:115376-115975  112 .   1.746   0.563   0.576   13.143  11.252  KS91    ASTARR  ASTARR_A:csaw:KS91
chr1    118501  118775  chr1:118501-118775  17  .   0.872   0.084   0.038   2.102   1.727   KS91    ASTARR  ASTARR_A:csaw:KS91
chr1    136226  136825  chr1:136226-136825  111 .   -2.27   0.661   0.021   13.065  11.192  KS91    ASTARR  ASTARR_R:csaw:KS91


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_csaw/fcc_astarr_macs_input_union.fcc_astarr_csaw_KS91.bed.gz

show first few lines of output:
chr1    10015   10442   chr1:10015-10442    chr1    9976    10475   chr1:9976-10475 62  .   -4.184  0.204   0.002   7.358   6.299   KS91    ASTARR  ASTARR_R:csaw:KS91  427
chr1    14253   14645   chr1:14253-14645    chr1    14226   14675   chr1:14226-14675    79  .   -6.187  0.209   0   9.192   7.917   KS91    ASTARR  ASTARR_R:csaw:KS91  392
chr1    16015   16477   chr1:16015-16477    chr1    15976   16525   chr1:15976-16525    42  .   -2.236  0.196   0.013   5.062   4.267   KS91    ASTARR  ASTARR_R:csaw:KS91  462
chr1    17237   17772   chr1:17237-17772    chr1    17201   17800   chr1:17201-17800    64  .   -1.944  0.79    0.021   7.506   6.429   KS91    ASTARR  ASTARR_R:csaw:KS91  535
chr1    28903   29613   chr1:28903-29613    chr1    28876   29650   chr1:28876-29650    76  .   -2.559  0.691   0.016   8.94    7.698   KS91    ASTARR  ASTARR_R:csaw:KS91  710
chr1    30803   31072   chr1:30803-31072    chr1    30776   31100   chr1:30776-31100    40  .   -2.501  0.252   0.003   4.826   4.06    KS91    ASTARR  ASTARR_R:csaw:KS91  269
chr1    101603  101849  chr1:101603-101849  chr1    101576  101875  chr1:101576-101875  14  .   -0.908  0.113   0.011   1.736   1.419   KS91    ASTARR  ASTARR_R:csaw:KS91  246
chr1    115411  115986  chr1:115411-115986  chr1    115376  115975  chr1:115376-115975  112 .   1.746   0.563   0.576   13.143  11.252  KS91    ASTARR  ASTARR_A:csaw:KS91  564
chr1    118518  118743  chr1:118518-118743  chr1    118501  118775  chr1:118501-118775  17  .   0.872   0.084   0.038   2.102   1.727   KS91    ASTARR  ASTARR_A:csaw:KS91  225
chr1    136071  137429  chr1:136071-137429  chr1    136226  136825  chr1:136226-136825  111 .   -2.27   0.661   0.021   13.065  11.192  KS91    ASTARR  ASTARR_R:csaw:KS91  599


Done!
Run Time: 11 seconds

Code

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep2.txt

Hostname:           plp-rcc-node-20
Slurm Array Index: 
Time Stamp:         07-21-25+16:03:04

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/fcc_astarr_macs_narrowpeak/K562.hg38.ASTARR.macs.KS91.Input.rep2.narrowpeak.bed.gz

show first few lines of input
chr1    10038   10442   chr1:10038-10442    334 .   3.45109 35.4672 33.48   73  ASTARR  Input.rep2  NarrowPeak
chr1    14282   14643   chr1:14282-14643    329 .   3.42712 34.9175 32.9339 178 ASTARR  Input.rep2  NarrowPeak
chr1    16017   16338   chr1:16017-16338    432 .   3.85851 45.2526 43.2099 226 ASTARR  Input.rep2  NarrowPeak
chr1    17267   17757   chr1:17267-17757    1927    .   8.41203 195.206 192.798 226 ASTARR  Input.rep2  NarrowPeak
chr1    28921   29612   chr1:28921-29612    1825    .   8.14841 184.983 182.591 397 ASTARR  Input.rep2  NarrowPeak
chr1    101625  101849  chr1:101625-101849  55  .   1.89331 7.15523 5.57621 77  ASTARR  Input.rep2  NarrowPeak
chr1    115421  115976  chr1:115421-115976  12303   .   28.3037 1233.77 1230.38 314 ASTARR  Input.rep2  NarrowPeak
chr1    136176  137423  chr1:136176-137423  3533    .   7.97211 355.946 353.344 623 ASTARR  Input.rep2  NarrowPeak
chr1    137737  139544  chr1:137737-139544  657 .   3.49285 67.8741 65.7373 1308    ASTARR  Input.rep2  NarrowPeak
chr1    180988  182058  chr1:180988-182058  945 .   5.65595 96.7751 94.5525 457 ASTARR  Input.rep2  NarrowPeak


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_union/fcc_astarr_macs_narrowpeak/fcc_astarr_macs_input_union.fcc_astarr_macs_input_rep2.bed.gz

show first few lines of output:
chr1    10015   10442   chr1:10015-10442    chr1    10038   10442   chr1:10038-10442    334 .   3.45109 35.4672 33.48   73  ASTARR  Input.rep2  NarrowPeak  404
chr1    14253   14645   chr1:14253-14645    chr1    14282   14643   chr1:14282-14643    329 .   3.42712 34.9175 32.9339 178 ASTARR  Input.rep2  NarrowPeak  361
chr1    16015   16477   chr1:16015-16477    chr1    16017   16338   chr1:16017-16338    432 .   3.85851 45.2526 43.2099 226 ASTARR  Input.rep2  NarrowPeak  321
chr1    17237   17772   chr1:17237-17772    chr1    17267   17757   chr1:17267-17757    1927    .   8.41203 195.206 192.798 226 ASTARR  Input.rep2  NarrowPeak  490
chr1    28903   29613   chr1:28903-29613    chr1    28921   29612   chr1:28921-29612    1825    .   8.14841 184.983 182.591 397 ASTARR  Input.rep2  NarrowPeak  691
chr1    101603  101849  chr1:101603-101849  chr1    101625  101849  chr1:101625-101849  55  .   1.89331 7.15523 5.57621 77  ASTARR  Input.rep2  NarrowPeak  224
chr1    115411  115986  chr1:115411-115986  chr1    115421  115976  chr1:115421-115976  12303   .   28.3037 1233.77 1230.38 314 ASTARR  Input.rep2  NarrowPeak  555
chr1    136071  137429  chr1:136071-137429  chr1    136176  137423  chr1:136176-137423  3533    .   7.97211 355.946 353.344 623 ASTARR  Input.rep2  NarrowPeak  1247
chr1    137737  139544  chr1:137737-139544  chr1    137737  139544  chr1:137737-139544  657 .   3.49285 67.8741 65.7373 1308    ASTARR  Input.rep2  NarrowPeak  1807
chr1    180982  182087  chr1:180982-182087  chr1    180988  182058  chr1:180988-182058  945 .   5.65595 96.7751 94.5525 457 ASTARR  Input.rep2  NarrowPeak  1070


Done!
Run Time: 9 seconds

Code

cat ${FD_LOG}/region.intersect.fcc_astarr_macs_input_overlap.genome_tss_pol2_rnaseq.txt

Hostname:           plp-rcc-node-19
Slurm Array Index: 
Time Stamp:         07-21-25+16:03:03

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/genome_tss/K562.hg38.TSS.selected_by_highest_Pol2_signal.filtered_by_RNAseq_TPM.bed.gz

show first few lines of input
chr1    29370   29371   chr1:29370-29371    WASH7P  2.3e-4  TSS_Pol2_RNAseq WASH7P
chr1    827522  827523  chr1:827522-827523  LINC00115   64.4656 TSS_Pol2_RNAseq LINC00115
chr1    827590  827591  chr1:827590-827591  LINC01128   64.4603 TSS_Pol2_RNAseq LINC01128
chr1    876802  876803  chr1:876802-876803  FAM41C  0.00788399  TSS_Pol2_RNAseq FAM41C
chr1    959256  959257  chr1:959256-959257  NOC2L   104.866 TSS_Pol2_RNAseq NOC2L
chr1    960583  960584  chr1:960583-960584  KLHL17  8.22571 TSS_Pol2_RNAseq KLHL17
chr1    1000097 1000098 chr1:1000097-1000098    HES4    50.5814 TSS_Pol2_RNAseq HES4
chr1    1013496 1013497 chr1:1013496-1013497    ISG15   42.9708 TSS_Pol2_RNAseq ISG15
chr1    1020119 1020120 chr1:1020119-1020120    AGRN    2.71433 TSS_Pol2_RNAseq AGRN
chr1    1116089 1116090 chr1:1116089-1116090    C1orf159    16.4374 TSS_Pol2_RNAseq C1orf159


Output:  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region_annotation/fcc_astarr_macs_input_overlap/genome_tss/fcc_astarr_macs_input_overlap.genome_tss_pol2_rnaseq.bed.gz

show first few lines of output:
chr1    28934   29499   chr1:28934-29499    chr1    29370   29371   chr1:29370-29371    WASH7P  2.3e-4  TSS_Pol2_RNAseq WASH7P  1
chr1    826796  828040  chr1:826796-828040  chr1    827522  827523  chr1:827522-827523  LINC00115   64.4656 TSS_Pol2_RNAseq LINC00115   1
chr1    826796  828040  chr1:826796-828040  chr1    827590  827591  chr1:827590-827591  LINC01128   64.4603 TSS_Pol2_RNAseq LINC01128   1
chr1    876493  877795  chr1:876493-877795  chr1    876802  876803  chr1:876802-876803  FAM41C  0.00788399  TSS_Pol2_RNAseq FAM41C  1
chr1    958722  959968  chr1:958722-959968  chr1    959256  959257  chr1:959256-959257  NOC2L   104.866 TSS_Pol2_RNAseq NOC2L   1
chr1    960468  961615  chr1:960468-961615  chr1    960583  960584  chr1:960583-960584  KLHL17  8.22571 TSS_Pol2_RNAseq KLHL17  1
chr1    998960  1001192 chr1:998960-1001192 chr1    1000097 1000098 chr1:1000097-1000098    HES4    50.5814 TSS_Pol2_RNAseq HES4    1
chr1    1013154 1014482 chr1:1013154-1014482    chr1    1013496 1013497 chr1:1013496-1013497    ISG15   42.9708 TSS_Pol2_RNAseq ISG15   1
chr1    1019190 1021734 chr1:1019190-1021734    chr1    1020119 1020120 chr1:1020119-1020120    AGRN    2.71433 TSS_Pol2_RNAseq AGRN    1
chr1    1115826 1116970 chr1:1115826-1116970    chr1    1116089 1116090 chr1:1116089-1116090    C1orf159    16.4374 TSS_Pol2_RNAseq C1orf159    1


Done!
Run Time: 4 seconds

Code

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

Hostname:           plp-rcc-node-05
Slurm Array Index: 
Time Stamp:         07-21-25+16:03:03

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/module_tf_shannon/K562.hg38.TF_Module.bed.gz

show first few lines of input
chr1    115702  115751  chr1:115702-115751  TF_Module   Module_02
chr1    115702  115751  chr1:115702-115751  TF_Module   Module_05
chr1    115702  115751  chr1:115702-115751  TF_Module   Module_10
chr1    115702  115751  chr1:115702-115751  TF_Module   Module_44
chr1    118585  118665  chr1:118585-118665  TF_Module   Module_47
chr1    136446  136510  chr1:136446-136510  TF_Module   Module_27
chr1    139031  139110  chr1:139031-139110  TF_Module   Module_02
chr1    139031  139110  chr1:139031-139110  TF_Module   Module_42
chr1    268005  268051  chr1:268005-268051  TF_Module   Module_02
chr1    268005  268051  chr1:268005-268051  TF_Module   Module_10


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

show first few lines of output:
chr1    115411  115986  chr1:115411-115986  chr1    115702  115751  chr1:115702-115751  TF_Module   Module_02   49
chr1    115411  115986  chr1:115411-115986  chr1    115702  115751  chr1:115702-115751  TF_Module   Module_05   49
chr1    115411  115986  chr1:115411-115986  chr1    115702  115751  chr1:115702-115751  TF_Module   Module_10   49
chr1    115411  115986  chr1:115411-115986  chr1    115702  115751  chr1:115702-115751  TF_Module   Module_44   49
chr1    118518  118743  chr1:118518-118743  chr1    118585  118665  chr1:118585-118665  TF_Module   Module_47   80
chr1    136071  137429  chr1:136071-137429  chr1    136446  136510  chr1:136446-136510  TF_Module   Module_27   64
chr1    137737  139544  chr1:137737-139544  chr1    139031  139110  chr1:139031-139110  TF_Module   Module_02   79
chr1    137737  139544  chr1:137737-139544  chr1    139031  139110  chr1:139031-139110  TF_Module   Module_42   79
chr1    267853  268603  chr1:267853-268603  chr1    268005  268051  chr1:268005-268051  TF_Module   Module_02   46
chr1    267853  268603  chr1:267853-268603  chr1    268005  268051  chr1:268005-268051  TF_Module   Module_10   46


Done!
Run Time: 4 seconds