Prepare Tiling MPRA data 01

Get K562 MPRA data files from Tewhey lab

In this analysis, we are using the unnormalized and normalized MPRA data processed and shared by Hannah from the Tewhey lab.

Set environment

source ../run_config_project.sh
show_env

You are working on             Duke Server: HARDAC
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 APP     (FD_APP):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/app
PROJECT REF     (FD_REF):      /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/references
PROJECT IMAGE   (FP_PRJ_SIF):  /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/app/singularity_proj_encode_fcc.sif

Check data

ls -d ${FD_DAT}/processed/MPRA_Tiling*

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/processed/MPRA_Tiling_K562_Tewhey_Hannah

FDIRY=${FD_DAT}/processed/MPRA_Tiling_K562_Tewhey_Hannah
FNAME=tiling_counts.tar.gz
FPATH=${FDIRY}/${FNAME}

ls ${FPATH} | xargs -n 1 basename

tiling_counts.tar.gz

Extract data

FDIRY=${FD_DAT}/processed/MPRA_Tiling_K562_Tewhey_Hannah
FNAME=tiling_counts.tar.gz
FPATH=${FDIRY}/${FNAME}

tar -xf ${FPATH} -C ${FDIRY}

Check results

ls -1 ${FD_DAT}/processed/MPRA_Tiling_K562_Tewhey_Hannah

tiling_counts
tiling_counts.tar.gz

ls ${FD_DAT}/processed/MPRA_Tiling_K562_Tewhey_Hannah/tiling_counts

FADS_tile_snp.20190214.attributes
OL13_20220512_counts.out
OL13_20220512_normalized_counts.out
OL43_20211228_counts.out
OL43_20211228_normalized_counts.out
OL43_20221003_counts.out
OL43_20221003_K562_normalized_counts.out
OL43.attributes
OL43_K562.bed
OL45_20220927_counts.out
OL45_20220927_K562_normalized_counts.out
OL45.attributes
OL45_K562.bed
UKBB_GTEx

ls ${FD_DAT}/processed/MPRA_Tiling_K562_Tewhey_Hannah/tiling_counts/UKBB_GTEx

OL27_20221220_K562_normalized_counts.out
OL28_20221220_K562_normalized_counts.out
OL29_20221220_K562_normalized_counts.out
OL30_20221220_K562_normalized_counts.out
OL31_20221220_K562_normalized_counts.out
OL32_20221220_K562_normalized_counts.out
OL33_20221220_K562_normalized_counts.out
OL41_20221220_SKNSH_normalized_counts.out
OL41_42_20221220_K562_normalized_counts.out
OL41B_20221220_HepG2_normalized_counts.out
OL42_20221220_HepG2_normalized_counts.out