Prepare ASTARR CSAW Peaks 01

Acquire data

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

echo ${FD_ALEX}

/data/reddylab/Alex

Code

FD_INP=${FD_ALEX}/tmp
FD_OUT=${FD_DAT}/processed/fcc_astarr_csaw

Check data

Code

FP_INPS=($(ls ${FD_INP}/atacSTARR.ultra_deep.6dna7rna*))
basename -a ${FP_INPS[@]}

atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.common_file_formatted.txt
atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.tsv
atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.windows.bed
atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.windows.txt
atacSTARR.ultra_deep.6dna7rna.csaw_tab_best.hg38.v10.tsv

Code

FP_INPS=($(ls ${FD_INP}/atacSTARR.ultra_deep.corrected*))
basename -a ${FP_INPS[@]}

atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.down.bed
atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.txt.gz
atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.up.bed
atacSTARR.ultra_deep.corrected.csaw.hg38.v10.tsv
atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.tsv
atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.windows.bed
atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.windows.txt
atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw_tab_best.hg38.v10.tsv

Copy to data source

Code

mkdir -p ${FD_OUT}
cp ${FD_INP}/atacSTARR.ultra_deep.corrected* ${FD_OUT}/

Code

mkdir -p ${FD_OUT}
cp ${FD_INP}/atacSTARR.ultra_deep.6dna7rna* ${FD_OUT}/

Check results

Code

ls -1 ${FD_DAT}/processed

CRISPRi_FlowFISH_K562_Riley_JinWoo
CRISPRi_Growth_K562_Gersbach_Alex
fcc_astarr_csaw
fcc_enhancer_Junke_zscore_240415
fcc_enhancer_Junke_zscore_240513_astarr_filter
fcc_enhancer_Junke_zscore_240611
fcc_trackhub_JinWoo
MPRA_Lenti_K562_Nadav_Vikram_230621
MPRA_Tiling_K562_Tewhey_Hannah
Readmd.md
STARR_ATAC_K562_Reddy_KS274_240311
STARR_ATAC_K562_Reddy_KS91_210401
STARR_WHG_K562_Reddy_A001_Alex
STARR_WHG_K562_Reddy_A001_Kari
TF_modules_Shannon

Code

ls -l ${FD_DAT}/processed/fcc_astarr_csaw

total 1364016
-rw-r--r-- 1 kk319 nogroup  29585549 May 12 15:39 atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.common_file_formatted.txt
-rw-r--r-- 1 kk319 nogroup  37906290 May 12 15:39 atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.tsv
-rw-r--r-- 1 kk319 nogroup 162923789 May 12 15:39 atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.windows.bed
-rw-r--r-- 1 kk319 nogroup 410557124 May 12 15:39 atacSTARR.ultra_deep.6dna7rna.csaw.hg38.v10.windows.txt
-rw-r--r-- 1 kk319 nogroup  52066228 May 12 15:39 atacSTARR.ultra_deep.6dna7rna.csaw_tab_best.hg38.v10.tsv
-rw-r--r-- 1 kk319 nogroup    821885 May 12 15:39 atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.down.bed
-rw-r--r-- 1 kk319 nogroup  29082966 May  9  2024 atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.txt
-rw-r--r-- 1 kk319 nogroup   8802019 May 12 15:39 atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.txt.gz
-rw-r--r-- 1 kk319 nogroup   1268836 May 12 15:39 atacSTARR.ultra_deep.corrected.csaw.hg38.v10.common_file_formatted.up.bed
-rw-r--r-- 1 kk319 nogroup  37180893 May 12 15:39 atacSTARR.ultra_deep.corrected.csaw.hg38.v10.tsv
-rw-r--r-- 1 kk319 nogroup  37180893 May 12 15:39 atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.tsv
-rw-r--r-- 1 kk319 nogroup 156656669 May 12 15:39 atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.windows.bed
-rw-r--r-- 1 kk319 nogroup 394467786 May 12 15:39 atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw.hg38.v10.windows.txt
-rw-r--r-- 1 kk319 nogroup  38222659 May 12 15:39 atacSTARR.ultra_deep.corrected.no_reps_5_and_6.csaw_tab_best.hg38.v10.tsv