Prepare Hi-C data 03 (intact Hi-C)

Check downloaded 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 variable

Code

TXT_FOLDER=hic_intact_K562_ENCSR479XDG

View data

Code

FDIRY=${FD_DAT}/external/${TXT_FOLDER}

echo   ${FDIRY}
ls -hs ${FDIRY}

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/hic_intact_K562_ENCSR479XDG
total 32G
220K K562.hg38.ENCSR479XDG.ENCFF126GED.hic_intact.contact_domain.bedpe.gz
2.8M K562.hg38.ENCSR479XDG.ENCFF256ZMD.hic_intact.loop.bedpe.gz
 32G K562.hg38.ENCSR479XDG.ENCFF621AIY.hic_intact.matrix.hic
 51M run_download.log.txt
4.0K run_download.sh

Hi-C loop calls

Code

FDIRY=${FD_DAT}/external/${TXT_FOLDER}
FNAME=K562.hg38.ENCSR479XDG.ENCFF256ZMD.hic_intact.loop.bedpe.gz
FPATH=${FDIRY}/${FNAME}

zcat ${FPATH} | head -5

#chr1   x1  x2  chr2    y1  y2  name    score   strand1 strand2 color   observed    expectedBL  expectedDonut   expectedH   expectedV   fdrBL   fdrDonut    fdrH    fdrV    numCollapsed    centroid1   centroid2   radius  highRes_start_1 highRes_end_1   highRes_start_2 highRes_end_2   localX  localY  localObserved   localPval   localPeakID
# juicer_tools version 2.13.07
chr10   102835000   102836000   chr10   102901000   102902000   .   .   .   .   0,255,255   16.0    2.5453029   2.0566912   2.896359    2.6027875   0.0 0.0 5.9604645E-8    0.0 2   102835000   102901500   500 102834600   102835200   102901400   102901700   102834700   102901500   4.0 2.17173181723318E-4 0
chr10   123583000   123584000   chr10   123967000   123968000   .   .   .   .   0,255,255   17.0    1.2294405   1.126373    1.5320965   2.968846    0.0 0.0 0.0 0.0 2   123583000   123967500   500 NA  NA  NA  NA  NA  NA  NA  NA  NA
chr10   60780000    60782000    chr10   60828000    60830000    .   .   .   .   0,255,255   16.0    3.9354546   3.6036625   4.087633    2.7198699   3.993511E-6 1.3113022E-6    6.377697E-6 5.9604645E-8    1   60781000    60829000    0   NA  NA  NA  NA  NA  NA  NA  NA  NA

Hi-C TAD calls

Code

FDIRY=${FD_DAT}/external/${TXT_FOLDER}
FNAME=K562.hg38.ENCSR479XDG.ENCFF126GED.hic_intact.contact_domain.bedpe.gz
FPATH=${FDIRY}/${FNAME}

zcat ${FPATH} | head -5

#chr1   x1  x2  chr2    y1  y2  name    score   strand1 strand2 color   score   uVarScore   lVarScore   upSign  loSign
# juicer_tools version 2.13.06
chr10   89790000    90730000    chr10   89790000    90730000    .   .   .   .   255,255,0   0.48733428805910184 0.43218752937273686 0.39101424267719964 0.4366181410974244  0.5132138857782754
chr10   117485000   118260000   chr10   117485000   118260000   .   .   .   .   255,255,0   0.47145995448002187 0.40388060738386966 0.40280872469677464 0.44690992767915844 0.4451019066403682
chr10   51125000    52215000    chr10   51125000    52215000    .   .   .   .   255,255,0   0.575707559391474   0.38559880334456653 0.3954850048221743  0.47122602168473726 0.40008340283569643