Prepare Tiling MPRA data 05

Liftover OL13 fragments from hg19 to hg38

Set environment

Code

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

Code

TXT_ASSAY=MPRA_Tiling_K562_Tewhey_Hannah

Check data

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment
FPATH=${FDIRY}/*hg19*
basename ${FPATH}

TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.bed.gz

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment_counts
FPATHS=($(ls ${FDIRY}/*hg19*))
basename -a ${FPATHS[@]}

TMPRA_K562_OL13_20220512.hg19.norm.Input.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep4.stranded_pos.bed.gz

Check script

Code

${FD_EXE}/run_liftOver.sh

liftOver - Move annotations from one assembly to another
usage:
   liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

***********************************************************************
WARNING: liftOver was only designed to work between different
         assemblies of the same organism. It may not do what you want
         if you are lifting between different organisms. If there has
         been a rearrangement in one of the species, the size of the
         region being mapped may change dramatically after mapping.
***********************************************************************

options:
   -minMatch=0.N Minimum ratio of bases that must remap. Default 0.95
   -gff  File is in gff/gtf format.  Note that the gff lines are converted
         separately.  It would be good to have a separate check after this
         that the lines that make up a gene model still make a plausible gene
         after liftOver
   -genePred - File is in genePred format
   -sample - File is in sample format
   -bedPlus=N - File is bed N+ format (i.e. first N fields conform to bed format)
   -positions - File is in browser "position" format
   -hasBin - File has bin value (used only with -bedPlus)
   -tab - Separate by tabs rather than space (used only with -bedPlus)
   -pslT - File is in psl format, map target side only
   -ends=N - Lift the first and last N bases of each record and combine the
             result. This is useful for lifting large regions like BAC end pairs.
   -minBlocks=0.N Minimum ratio of alignment blocks or exons that must map
                  (default 1.00)
   -fudgeThick    (bed 12 or 12+ only) If thickStart/thickEnd is not mapped,
                  use the closest mapped base.  Recommended if using 
                  -minBlocks.
   -multiple               Allow multiple output regions
   -noSerial               In -multiple mode, do not put a serial number in the 5th BED column
   -minChainT, -minChainQ  Minimum chain size in target/query, when mapping
                           to multiple output regions (default 0, 0)
   -minSizeT               deprecated synonym for -minChainT (ENCODE compat.)
   -minSizeQ               Min matching region size in query with -multiple.
   -chainTable             Used with -multiple, format is db.tablename,
                               to extend chains from net (preserves dups)
   -errorHelp              Explain error messages

: 255

Execute: LiftOver fragment

Test file IO

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment

FP_INP=${FDIRY}/*hg19*
FN_INP=$(basename ${FP_INP})

FN_OUT_LIFTED=${FN_INP/hg19/hg38}
FN_TMP_LIFTED=${FN_OUT_LIFTED%.*}
FN_OUT_UNLIFT=${FN_INP/hg19/unlifted}
FN_TMP_UNLIFT=${FN_OUT_UNLIFT%.*}

echo ${FN_INP}
echo ${FN_OUT_LIFTED}
echo ${FN_TMP_LIFTED}
echo ${FN_OUT_UNLIFT}
echo ${FN_TMP_UNLIFT}

TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.stranded_pos.bed

run liftOver

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment

FP_INP=${FDIRY}/*hg19*
FN_INP=$(basename ${FP_INP})

FN_OUT_LIFTED=${FN_INP/hg19/hg38}
FN_OUT_UNLIFT=${FN_INP/hg19/unlifted}

${FD_EXE}/run_liftOver.sh \
    -bedPlus=6 \
    ${FDIRY}/${FN_INP} \
    /data/reddylab/Reference_Data/Genomes/hg38/hg19ToHg38.over.chain \
    ${FDIRY}/${FN_TMP_LIFTED} \
    ${FDIRY}/${FN_TMP_UNLIFT}

Reading liftover chains
Mapping coordinates

Code

gzip -f ${FDIRY}/${FN_TMP_UNLIFT}
gzip -f ${FDIRY}/${FN_TMP_LIFTED}

Check results

Code

ls ${FDIRY}

TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.stranded_pos.bed.gz
TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.bed.gz
TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.bed.gz

Code

zcat ${FDIRY}/${FN_INP}        | wc -l 
zcat ${FDIRY}/${FN_OUT_LIFTED} | wc -l 
zcat ${FDIRY}/${FN_OUT_UNLIFT} | wc -l

21914
21914
0

Execute: LiftOver fragment count

Test loop and file IO

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment_counts
FPATHS=($(ls ${FDIRY}/*hg19*))

for FP_INP in ${FPATHS[@]}; do
    ###
    FN_INP=$(basename ${FP_INP})
    FN_OUT_LIFTED=${FN_INP/hg19/hg38}
    FN_OUT_UNLIFT=${FN_INP/hg19/unlifted}
    FN_TMP_LIFTED=${FN_OUT_LIFTED%.*}
    FN_TMP_UNLIFT=${FN_OUT_UNLIFT%.*}

    echo ${FN_INP}
    echo ${FN_OUT_LIFTED}
    echo ${FN_TMP_LIFTED}
    echo ${FN_OUT_UNLIFT}
    echo ${FN_TMP_UNLIFT}
    
    echo ==================
done

TMPRA_K562_OL13_20220512.hg19.norm.Input.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.mean.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Input.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Input.mean.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep1.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep1.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep2.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep2.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep3.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep3.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Input.rep4.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Input.rep4.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Log2FC.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Log2FC.mean.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Log2FC.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Log2FC.mean.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.mean.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Output.mean.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Output.mean.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep1.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep1.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep2.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep2.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep3.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep3.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.norm.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.norm.Output.rep4.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.norm.Output.rep4.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep1.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep1.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep2.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep2.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep3.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep3.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Input.rep4.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Input.rep4.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep1.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep1.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep1.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep2.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep2.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep2.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep3.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep3.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep3.stranded_pos.bed
==================
TMPRA_K562_OL13_20220512.hg19.raw.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.hg38.raw.Output.rep4.stranded_pos.bed
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep4.stranded_pos.bed.gz
TMPRA_K562_OL13_20220512.unlifted.raw.Output.rep4.stranded_pos.bed
==================

run liftOver and check results

Code

FDIRY=${FD_RES}/assay_fcc/${TXT_ASSAY}/fragment_counts
FPATHS=($(ls ${FDIRY}/*hg19*))

for FP_INP in ${FPATHS[@]}; do
    ### setup
    FN_INP=$(basename ${FP_INP})
    FN_OUT_LIFTED=${FN_INP/hg19/hg38}
    FN_OUT_UNLIFT=${FN_INP/hg19/unlifted}
    FN_TMP_LIFTED=${FN_OUT_LIFTED%.*}
    FN_TMP_UNLIFT=${FN_OUT_UNLIFT%.*}
    
    ### liftover
    ${FD_EXE}/run_liftOver.sh \
        -bedPlus=6 \
        ${FDIRY}/${FN_INP} \
        /data/reddylab/Reference_Data/Genomes/hg38/hg19ToHg38.over.chain \
        ${FDIRY}/${FN_TMP_LIFTED} \
        ${FDIRY}/${FN_TMP_UNLIFT}
    
    ### compress files
    gzip -f ${FDIRY}/${FN_TMP_UNLIFT}
    gzip -f ${FDIRY}/${FN_TMP_LIFTED}
    
    ### show
    echo "Input: " ${FN_INP}
    echo "Output:" ${FN_OUT_LIFTED}
    zcat ${FDIRY}/${FN_INP}        | wc -l
    zcat ${FDIRY}/${FN_OUT_LIFTED} | wc -l
    zcat ${FDIRY}/${FN_OUT_UNLIFT} | wc -l
    echo ==================
done

Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Input.mean.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Input.mean.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Input.rep1.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Input.rep1.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Input.rep2.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Input.rep2.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Input.rep3.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Input.rep3.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Input.rep4.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Input.rep4.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Log2FC.mean.stranded_pos.bed.gz
21757
21757
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Output.mean.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Output.rep1.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Output.rep1.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Output.rep2.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Output.rep2.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Output.rep3.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Output.rep3.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.norm.Output.rep4.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.norm.Output.rep4.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Input.rep1.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Input.rep1.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Input.rep2.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Input.rep2.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Input.rep3.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Input.rep3.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Input.rep4.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Input.rep4.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Output.rep1.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Output.rep1.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Output.rep2.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Output.rep2.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Output.rep3.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Output.rep3.stranded_pos.bed.gz
21914
21914
0
==================
Reading liftover chains
Mapping coordinates
Input:  TMPRA_K562_OL13_20220512.hg19.raw.Output.rep4.stranded_pos.bed.gz
Output: TMPRA_K562_OL13_20220512.hg38.raw.Output.rep4.stranded_pos.bed.gz
21914
21914
0
==================