Prepare Hi-C data 03 (in situ 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_insitu_K562_ENCSR545YBD

View data

Code

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

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

/data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/hic_insitu_K562_ENCSR545YBD
total 22G
296K K562.hg38.ENCSR545YBD.ENCFF271SAF.hic_insitu.contact_domain.bedpe.gz
 22G K562.hg38.ENCSR545YBD.ENCFF616PUW.hic_insitu.matrix.hic
880K K562.hg38.ENCSR545YBD.ENCFF693XIL.hic_insitu.loop.bedpe.gz
 34M run_download.log.txt
4.0K run_download.sh

Hi-C loop calls

Code

FDIRY=${FD_DAT}/external/${TXT_FOLDER}
FNAME=K562.hg38.ENCSR545YBD.ENCFF693XIL.hic_insitu.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
# juicer_tools version 2.13.06
chr10   34010000    34020000    chr10   35050000    35060000    .   .   .   .   0,255,255   25.0    6.6749783   6.117001    6.028173    4.855595    0.0036679406    3.0621103E-4    3.4923825E-4    6.161639E-6 1   34015000    35055000    0
chr10   124000000   124005000   chr10   124380000   124385000   .   .   .   .   0,255,255   38.0    13.690522   14.195029   18.101181   18.336344   0.0022106771    0.0023932518    0.058508653 0.059743028 3   123997500   124387500   7071
chr10   133330000   133335000   chr10   133495000   133500000   .   .   .   .   0,255,255   39.0    14.323421   15.468441   18.856985   18.800962   0.0011134844    0.0011820481    0.037496306 0.038466662 2   133330000   133500000   3536

Hi-C TAD calls

Code

FDIRY=${FD_DAT}/external/${TXT_FOLDER}
FNAME=K562.hg38.ENCSR545YBD.ENCFF271SAF.hic_insitu.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   84565000    86085000    chr10   84565000    86085000    .   .   .   .   255,255,0   0.797322669093712   0.36036680286901346 0.34029928924052977 0.44465944272445823 0.547858617131063
chr10   50985000    52225000    chr10   50985000    52225000    .   .   .   .   255,255,0   1.0083018408826874  0.3171058429109649  0.34772601741376474 0.5433548387096774  0.4545161290322581
chr10   98415000    99300000    chr10   98415000    99300000    .   .   .   .   255,255,0   0.6516994003966435  0.2746901933484111  0.28586117952993195 0.4402221941674031  0.6153263476833734