Prepare ENCODE ChIP-seq Histone 12

Export signal data to result folder

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 variable

Code

REGION_FOLDER_DAT="encode_chipseq_histone_250120"
REGION_FOLDER_RES="encode_chipseq_histone"

View data

Code

ls ${FD_DAT}/external/

chrom.hg38.main.bed              encode_crispri_hcrff
chrom.hg38.total.bed             encode_open_chromatin
chrom.sizes.hg19                 encode_rnaseq
chrom.sizes.hg38                 genome_tss
encode_chipseq_agarwal2023       hic_insitu_GM12878
encode_chipseq_flagship          hic_insitu_K562_ENCSR545YBD
encode_chipseq_histone_241223    hic_intact_K562_deep
encode_chipseq_histone_250120    hic_intact_K562_ENCSR479XDG
encode_chipseq_histone_previous  protein_interpro
encode_chipseq_subset            RNAseq
encode_chipseq_tf_250120         tmp
encode_chromatin_states

Code

FDIRY=${FD_DAT}/external/${REGION_FOLDER_DAT}
echo  ${FDIRY}
ls -1 ${FDIRY}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_chipseq_histone_250120
metadata.merged.tsv
region_narrowPeak
signal_fold_change
signal_pvalue

Code

FDIRY=${FD_DAT}/external/${REGION_FOLDER_DAT}
ls -1 ${FDIRY}/signal_fold_change

checksum_md5sum.txt
checksum_results.txt
ENCFF139KZL.bigWig
ENCFF242ENK.bigWig
ENCFF253TOF.bigWig
ENCFF286WRJ.bigWig
ENCFF317VHO.bigWig
ENCFF347YYH.bigWig
ENCFF381NDD.bigWig
ENCFF399SGM.bigWig
ENCFF544AVW.bigWig
ENCFF583BKU.bigWig
ENCFF601JGK.bigWig
ENCFF605FAF.bigWig
ENCFF607SUJ.bigWig
ENCFF621DJP.bigWig
ENCFF654SLZ.bigWig
ENCFF660WUG.bigWig
ENCFF806YEZ.bigWig
ENCFF911JVK.bigWig
ENCFF959YJV.bigWig
files.txt
metadata.tsv

Link to the Results folder

Code

FDIRY=${FD_RES}/assay_chipseq
echo  ${FDIRY}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/assay_chipseq

Code

FDIRY=${FD_RES}/assay_chipseq/${REGION_FOLDER_RES}/summary

echo     ${FDIRY}
mkdir -p ${FDIRY}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/assay_chipseq/encode_chipseq_histone/summary

Code

FD_INP=${FD_DAT}/external/${REGION_FOLDER_DAT}
FD_OUT=${FD_RES}/assay_chipseq/${REGION_FOLDER_RES}

FP_SRC=${FD_INP}/signal_fold_change
FP_LNK=${FD_OUT}/signal_fold_change

ln -s ${FP_SRC} ${FP_LNK}

View results

Code

ls ${FD_OUT}

signal_fold_change  summary

Code

ls ${FD_OUT}/signal_fold_change

checksum_md5sum.txt   ENCFF381NDD.bigWig  ENCFF654SLZ.bigWig
checksum_results.txt  ENCFF399SGM.bigWig  ENCFF660WUG.bigWig
ENCFF139KZL.bigWig    ENCFF544AVW.bigWig  ENCFF806YEZ.bigWig
ENCFF242ENK.bigWig    ENCFF583BKU.bigWig  ENCFF911JVK.bigWig
ENCFF253TOF.bigWig    ENCFF601JGK.bigWig  ENCFF959YJV.bigWig
ENCFF286WRJ.bigWig    ENCFF605FAF.bigWig  files.txt
ENCFF317VHO.bigWig    ENCFF607SUJ.bigWig  metadata.tsv
ENCFF347YYH.bigWig    ENCFF621DJP.bigWig