Prepare Tiling MPRA data 04

Covert count matrix to bed format

Set environment

Code 
suppressMessages(suppressWarnings(source("../run_config_project_sing.R")))
show_env()
You are working on        Singularity 
BASE DIRECTORY (FD_BASE): /mount 
REPO DIRECTORY (FD_REPO): /mount/repo 
WORK DIRECTORY (FD_WORK): /mount/work 
DATA DIRECTORY (FD_DATA): /mount/data 

You are working with      ENCODE FCC 
PATH OF PROJECT (FD_PRJ): /mount/repo/Proj_ENCODE_FCC 
PROJECT RESULTS (FD_RES): /mount/repo/Proj_ENCODE_FCC/results 
PROJECT SCRIPTS (FD_EXE): /mount/repo/Proj_ENCODE_FCC/scripts 
PROJECT DATA    (FD_DAT): /mount/repo/Proj_ENCODE_FCC/data 
PROJECT NOTE    (FD_NBK): /mount/repo/Proj_ENCODE_FCC/notebooks 
PROJECT DOCS    (FD_DOC): /mount/repo/Proj_ENCODE_FCC/docs 
PROJECT LOG     (FD_LOG): /mount/repo/Proj_ENCODE_FCC/log 
PROJECT APP     (FD_APP): /mount/repo/Proj_ENCODE_FCC/app 
PROJECT REF     (FD_REF): /mount/repo/Proj_ENCODE_FCC/references

Global variables

Code 
TXT_ASSAY_TYPE = "assay_fcc"
TXT_ASSAY_NAME = "MPRA_Tiling_K562_Tewhey_Hannah"

Import data

Check data files

Code 
txt_folder = "fragment_counts/summary"
txt_fdiry  = file.path(FD_RES, TXT_ASSAY_TYPE, TXT_ASSAY_NAME, txt_folder)
vec = dir(txt_fdiry)
for (txt in vec){cat(txt, "\n")}
TMPRA_K562_OL13_20220512.hg19.norm.stranded_pos.tsv 
TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.tsv 
TMPRA_K562_OL43_20221003.hg38.norm.stranded_pos.tsv 
TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.tsv 
TMPRA_K562_OL45_20220927.hg38.norm.stranded_pos.tsv 
TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.tsv

Import data

Code 
### init
txt_folder = "fragment_counts/summary"
txt_strand = "stranded_pos"
txt_fdiry  = file.path(FD_RES, TXT_ASSAY_TYPE, TXT_ASSAY_NAME, txt_folder)

vec_txt_prefix = c(
    'TMPRA_K562_OL13_20220512.hg19.raw',
    'TMPRA_K562_OL13_20220512.hg19.norm',
    'TMPRA_K562_OL43_20221003.hg38.raw',
    'TMPRA_K562_OL43_20221003.hg38.norm',
    'TMPRA_K562_OL45_20220927.hg38.raw',
    'TMPRA_K562_OL45_20220927.hg38.norm'
)

### read table
lst_dat_read = lapply(vec_txt_prefix, function(txt_prefix){
    ### setup file name and path
    txt_fname = paste(
        txt_prefix, 
        txt_strand, 
        "tsv", 
        sep=".")
    txt_fpath = file.path(txt_fdiry, txt_fname)

    ### show progress
    cat("Read table:", txt_fname, "\n")
    
    ### read table
    dat = read_tsv(txt_fpath, show_col_types = FALSE)
    return(dat)
})

names(lst_dat_read) = vec_txt_prefix
Read table: TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.tsv 
Read table: TMPRA_K562_OL13_20220512.hg19.norm.stranded_pos.tsv 
Read table: TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.tsv 
Read table: TMPRA_K562_OL43_20221003.hg38.norm.stranded_pos.tsv 
Read table: TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.tsv 
Read table: TMPRA_K562_OL45_20220927.hg38.norm.stranded_pos.tsv

Check imported data

Code 
lst = lst_dat_read
txt = names(lst)[1]
dat = lst[[txt]]
cat(txt, "\n")
fun_display_table(head(dat, 6))
TMPRA_K562_OL13_20220512.hg19.raw
Name Chrom ChromStart ChromEnd Strand Input.rep1 Input.rep2 Input.rep3 Input.rep4 Output.rep1 Output.rep2 Output.rep3 Output.rep4
chr11:61554801-61555000 chr11 61554801 61555000 + 971 542 785 640 112 236 220 204
chr11:61554806-61555005 chr11 61554806 61555005 + 1267 562 1059 564 211 103 390 215
chr11:61554811-61555010 chr11 61554811 61555010 + 1183 641 1118 655 261 476 98 276
chr11:61554816-61555015 chr11 61554816 61555015 + 1020 476 1086 584 137 177 274 497
chr11:61554821-61555020 chr11 61554821 61555020 + 1138 580 894 565 187 108 360 365
chr11:61554826-61555025 chr11 61554826 61555025 + 702 406 745 318 82 163 195 66
Code 
lst = lst_dat_read
txt = names(lst)[2]
dat = lst[[txt]]
cat(txt, "\n")
fun_display_table(head(dat, 6))
TMPRA_K562_OL13_20220512.hg19.norm
Name Chrom ChromStart ChromEnd Strand Input.rep1 Input.rep2 Input.rep3 Input.rep4 Output.rep1 Output.rep2 Output.rep3 Output.rep4 Input.mean Output.mean Log2FC.mean
chr11:61554801-61555000 chr11 61554801 61555000 + 532.1798 531.0790 481.0834 621.4943 239.6332 475.0396 279.9729 249.11100 541.4591 310.9392 -0.8002201
chr11:61554806-61555005 chr11 61554806 61555005 + 694.4097 550.6760 649.0029 547.6919 451.4519 207.3266 496.3155 262.54346 610.4451 354.4094 -0.7844449
chr11:61554811-61555010 chr11 61554811 61555010 + 648.3715 628.0842 685.1608 636.0606 558.4310 958.1307 124.7152 337.03253 649.4193 494.5773 -0.3929540
chr11:61554816-61555015 chr11 61554816 61555015 + 559.0354 466.4089 665.5498 567.1136 293.1228 356.2797 348.6935 606.90279 564.5269 401.2497 -0.4925421
chr11:61554821-61555020 chr11 61554821 61555020 + 623.7081 568.3133 547.8835 548.6629 400.1019 217.3910 458.1374 445.71331 572.1420 380.3359 -0.5890991
chr11:61554826-61555025 chr11 61554826 61555025 + 384.7479 397.8193 456.5696 308.8050 175.4457 328.0994 248.1578 80.59474 386.9855 208.0744 -0.8951798
Code 
names(lst)
  1. 'TMPRA_K562_OL13_20220512.hg19.raw'
  2. 'TMPRA_K562_OL13_20220512.hg19.norm'
  3. 'TMPRA_K562_OL43_20221003.hg38.raw'
  4. 'TMPRA_K562_OL43_20221003.hg38.norm'
  5. 'TMPRA_K562_OL45_20220927.hg38.raw'
  6. 'TMPRA_K562_OL45_20220927.hg38.norm'
Code 
dat = lst[[5]]
print(table(dat$Chrom))
head(dat)

chr11 chr16  chr2 chr20 
39848 11438 19914 19892
A tibble: 6 × 13
Name Chrom ChromStart ChromEnd Strand Input.rep1 Input.rep2 Input.rep3 Input.rep4 Output.rep1 Output.rep2 Output.rep3 Output.rep4
<chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
chr11:4505501-4505700 chr11 4505501 4505700 + 811 664 917 815 643 665 612 714
chr11:4505601-4505800 chr11 4505601 4505800 + 693 552 607 551 413 204 279 395
chr11:4505701-4505900 chr11 4505701 4505900 + 577 414 448 371 303 241 217 291
chr11:4505801-4506000 chr11 4505801 4506000 + 855 754 688 812 366 315 340 406
chr11:4505901-4506100 chr11 4505901 4506100 + 317 217 313 280 117 115 102 179
chr11:4506001-4506200 chr11 4506001 4506200 + 444 422 454 473 237 237 215 383

Save results

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Counts: OL13_20220512

OL13_20220512.hg19.raw.Input .rep[1-4].stranded_pos.bed
OL13_20220512.hg19.raw.Output.rep[1-4].stranded_pos.bed

OL13_20220512.hg19.norm.Input .mean.stranded_pos.bed
OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed
OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Counts: OL43_20221003

OL43_20221003.hg38.raw.Input .rep[1-6].stranded_pos.bed
OL43_20221003.hg38.raw.Output.rep[1-5].stranded_pos.bed

OL43_20221003.hg38.norm.Input .rep[1-6].stranded_pos.bed
OL43_20221003.hg38.norm.Output.rep[1-5].stranded_pos.bed

OL43_20221003.hg38.norm.Input .mean.stranded_pos.bed
OL43_20221003.hg38.norm.Output.mean.stranded_pos.bed
OL43_20221003.hg38.norm.Log2FC.mean.stranded_pos.bed

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Counts: OL45_20220927

OL43_20221003.hg38.raw. Input .rep[1-4].stranded_pos.bed
OL43_20221003.hg38.norm.Output.rep[1-4].stranded_pos.bed

OL43_20221003.hg38.norm.Input .rep[1-4].stranded_pos.bed
OL43_20221003.hg38.norm.Output.rep[1-4].stranded_pos.bed

OL43_20221003.hg38.norm.Input .mean.stranded_pos.bed
OL43_20221003.hg38.norm.Output.mean.stranded_pos.bed
OL43_20221003.hg38.norm.Log2FC.mean.stranded_pos.bed


+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<Results>
PROJECT/results/assay_fcc
└── MPRA_Tiling_K562_TewheyHhannah
    └── fragment_counts
        ├── TMPRA_K562_OL13_20220512.hg19.raw.Input.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.raw.Output.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.norm.Input.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.norm.Output.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.norm.Input.mean.stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed
        ├── TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.raw.Input.rep[1-6].stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.raw.Output.rep[1-5].stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.norm.Input.rep[1-6].stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.norm.Output.rep[1-5].stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.norm.Input.mean.stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.norm.Output.mean.stranded_pos.bed
        ├── TMPRA_K562_OL43_20221003.hg38.norm.Log2FC.mean.stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.raw.Input.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.raw.Output.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.norm.Input.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.norm.Output.rep[1-4].stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.norm.Input.mean.stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.norm.Output.mean.stranded_pos.bed
        ├── TMPRA_K562_OL45_20220927.hg38.norm.Log2FC.mean.stranded_pos.bed
        └── summary
            ├── TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.tsv
            ├── TMPRA_K562_OL13_20220512.hg19.norm.stranded_pos.tsv
            ├── TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.tsv
            ├── TMPRA_K562_OL43_20221003.hg38.norm.stranded_pos.tsv
            ├── TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.tsv
            └── TMPRA_K562_OL45_20220927.hg38.norm.stranded_pos.tsv
Code 
### init
txt_folder = "fragment_counts"
txt_strand = "stranded_pos"
txt_fdiry  = file.path(FD_RES, TXT_ASSAY_TYPE, TXT_ASSAY_NAME, txt_folder)

###
cat("Output directory:", "\n")
cat(txt_fdiry, "\n")

###
lst_dat = lst_dat_read
for (txt_prefix in names(lst_dat)){
    
    ### split a table by score columns
    dat = lst_dat[[txt_prefix]]
    dat = dat %>% 
        dplyr::filter(Strand == "+") %>% 
        gather(Sample, Score, -Chrom, -ChromStart, -ChromEnd, -Name, -Strand)
    lst = split(dat, dat$Sample)
    
    ### save each score column into a bed file
    for (txt_cname in names(lst)){
        ### setup data for each column
        dat = lst[[txt_cname]]
        dat = dat %>%
            dplyr::select(Chrom, ChromStart, ChromEnd, Name, Score, Strand) %>%
            dplyr::filter(!is.infinite(Score)) %>% 
            dplyr::mutate(Score = round(Score, 3)) %>%
            dplyr::arrange(Chrom, ChromStart, ChromEnd)

        ### store into a bed file
        txt_fname = paste(txt_prefix, txt_cname, txt_strand, "bed.gz", sep=".")
        txt_fpath = file.path(txt_fdiry, txt_fname)
        write_tsv(dat, txt_fpath, col_names=FALSE)

        cat("\n++++++++++++++++++++++++++++++++++++++++++\n")
        cat("Save bed file:", txt_fname, "\n")
        flush.console()
        
        fun_display_table(head(dat, 3))
        flush.console()
    }
}
Output directory: 
/mount/repo/Proj_ENCODE_FCC/results/assay_fcc/MPRA_Tiling_K562_Tewhey_Hannah/fragment_counts 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 971 +
chr11 61554806 61555005 chr11:61554806-61555005 1267 +
chr11 61554811 61555010 chr11:61554811-61555010 1183 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 542 +
chr11 61554806 61555005 chr11:61554806-61555005 562 +
chr11 61554811 61555010 chr11:61554811-61555010 641 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 785 +
chr11 61554806 61555005 chr11:61554806-61555005 1059 +
chr11 61554811 61555010 chr11:61554811-61555010 1118 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 640 +
chr11 61554806 61555005 chr11:61554806-61555005 564 +
chr11 61554811 61555010 chr11:61554811-61555010 655 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 112 +
chr11 61554806 61555005 chr11:61554806-61555005 211 +
chr11 61554811 61555010 chr11:61554811-61555010 261 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 236 +
chr11 61554806 61555005 chr11:61554806-61555005 103 +
chr11 61554811 61555010 chr11:61554811-61555010 476 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 220 +
chr11 61554806 61555005 chr11:61554806-61555005 390 +
chr11 61554811 61555010 chr11:61554811-61555010 98 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.raw.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 204 +
chr11 61554806 61555005 chr11:61554806-61555005 215 +
chr11 61554811 61555010 chr11:61554811-61555010 276 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Input.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 541.459 +
chr11 61554806 61555005 chr11:61554806-61555005 610.445 +
chr11 61554811 61555010 chr11:61554811-61555010 649.419 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 532.180 +
chr11 61554806 61555005 chr11:61554806-61555005 694.410 +
chr11 61554811 61555010 chr11:61554811-61555010 648.371 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 531.079 +
chr11 61554806 61555005 chr11:61554806-61555005 550.676 +
chr11 61554811 61555010 chr11:61554811-61555010 628.084 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 481.083 +
chr11 61554806 61555005 chr11:61554806-61555005 649.003 +
chr11 61554811 61555010 chr11:61554811-61555010 685.161 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 621.494 +
chr11 61554806 61555005 chr11:61554806-61555005 547.692 +
chr11 61554811 61555010 chr11:61554811-61555010 636.061 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 -0.800 +
chr11 61554806 61555005 chr11:61554806-61555005 -0.784 +
chr11 61554811 61555010 chr11:61554811-61555010 -0.393 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 310.939 +
chr11 61554806 61555005 chr11:61554806-61555005 354.409 +
chr11 61554811 61555010 chr11:61554811-61555010 494.577 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 239.633 +
chr11 61554806 61555005 chr11:61554806-61555005 451.452 +
chr11 61554811 61555010 chr11:61554811-61555010 558.431 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 475.040 +
chr11 61554806 61555005 chr11:61554806-61555005 207.327 +
chr11 61554811 61555010 chr11:61554811-61555010 958.131 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 279.973 +
chr11 61554806 61555005 chr11:61554806-61555005 496.316 +
chr11 61554811 61555010 chr11:61554811-61555010 124.715 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL13_20220512.hg19.norm.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 61554801 61555000 chr11:61554801-61555000 249.111 +
chr11 61554806 61555005 chr11:61554806-61555005 262.543 +
chr11 61554811 61555010 chr11:61554811-61555010 337.033 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 1190 +
chr8 126735951 126736150 chr8:126735951-126736150 194 +
chr8 126736001 126736200 chr8:126736001-126736200 746 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 1409 +
chr8 126735951 126736150 chr8:126735951-126736150 161 +
chr8 126736001 126736200 chr8:126736001-126736200 757 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 1259 +
chr8 126735951 126736150 chr8:126735951-126736150 161 +
chr8 126736001 126736200 chr8:126736001-126736200 708 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 1179 +
chr8 126735951 126736150 chr8:126735951-126736150 208 +
chr8 126736001 126736200 chr8:126736001-126736200 704 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep5.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 665 +
chr8 126735951 126736150 chr8:126735951-126736150 95 +
chr8 126736001 126736200 chr8:126736001-126736200 350 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Input.rep6.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 644 +
chr8 126735951 126736150 chr8:126735951-126736150 78 +
chr8 126736001 126736200 chr8:126736001-126736200 379 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 5410 +
chr8 126735951 126736150 chr8:126735951-126736150 440 +
chr8 126736001 126736200 chr8:126736001-126736200 2328 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 3846 +
chr8 126735951 126736150 chr8:126735951-126736150 398 +
chr8 126736001 126736200 chr8:126736001-126736200 1654 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 6325 +
chr8 126735951 126736150 chr8:126735951-126736150 692 +
chr8 126736001 126736200 chr8:126736001-126736200 3308 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 4822 +
chr8 126735951 126736150 chr8:126735951-126736150 485 +
chr8 126736001 126736200 chr8:126736001-126736200 2493 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.raw.Output.rep5.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 4941 +
chr8 126735951 126736150 chr8:126735951-126736150 595 +
chr8 126736001 126736200 chr8:126736001-126736200 2652 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 815.679 +
chr8 126735951 126736150 chr8:126735951-126736150 114.311 +
chr8 126736001 126736200 chr8:126736001-126736200 466.543 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 801.261 +
chr8 126735951 126736150 chr8:126735951-126736150 130.626 +
chr8 126736001 126736200 chr8:126736001-126736200 502.303 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 839.773 +
chr8 126735951 126736150 chr8:126735951-126736150 95.957 +
chr8 126736001 126736200 chr8:126736001-126736200 451.177 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 807.082 +
chr8 126735951 126736150 chr8:126735951-126736150 103.209 +
chr8 126736001 126736200 chr8:126736001-126736200 453.864 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 740.868 +
chr8 126735951 126736150 chr8:126735951-126736150 130.704 +
chr8 126736001 126736200 chr8:126736001-126736200 442.384 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep5.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 867.134 +
chr8 126735951 126736150 chr8:126735951-126736150 123.876 +
chr8 126736001 126736200 chr8:126736001-126736200 456.386 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Input.rep6.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 837.958 +
chr8 126735951 126736150 chr8:126735951-126736150 101.492 +
chr8 126736001 126736200 chr8:126736001-126736200 493.146 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Log2FC.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 3.197 +
chr8 126735951 126736150 chr8:126735951-126736150 2.740 +
chr8 126736001 126736200 chr8:126736001-126736200 2.963 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 7477.752 +
chr8 126735951 126736150 chr8:126735951-126736150 763.552 +
chr8 126736001 126736200 chr8:126736001-126736200 3636.737 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 8392.241 +
chr8 126735951 126736150 chr8:126735951-126736150 682.548 +
chr8 126736001 126736200 chr8:126736001-126736200 3611.301 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 6873.620 +
chr8 126735951 126736150 chr8:126735951-126736150 711.311 +
chr8 126736001 126736200 chr8:126736001-126736200 2956.050 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 6826.874 +
chr8 126735951 126736150 chr8:126735951-126736150 746.909 +
chr8 126736001 126736200 chr8:126736001-126736200 3570.482 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 8314.847 +
chr8 126735951 126736150 chr8:126735951-126736150 836.313 +
chr8 126736001 126736200 chr8:126736001-126736200 4298.821 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL43_20221003.hg38.norm.Output.rep5.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr8 126735901 126736100 chr8:126735901-126736100 6981.177 +
chr8 126735951 126736150 chr8:126735951-126736150 840.680 +
chr8 126736001 126736200 chr8:126736001-126736200 3747.031 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 811 +
chr11 4505601 4505800 chr11:4505601-4505800 693 +
chr11 4505701 4505900 chr11:4505701-4505900 577 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 664 +
chr11 4505601 4505800 chr11:4505601-4505800 552 +
chr11 4505701 4505900 chr11:4505701-4505900 414 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 917 +
chr11 4505601 4505800 chr11:4505601-4505800 607 +
chr11 4505701 4505900 chr11:4505701-4505900 448 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 815 +
chr11 4505601 4505800 chr11:4505601-4505800 551 +
chr11 4505701 4505900 chr11:4505701-4505900 371 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 643 +
chr11 4505601 4505800 chr11:4505601-4505800 413 +
chr11 4505701 4505900 chr11:4505701-4505900 303 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 665 +
chr11 4505601 4505800 chr11:4505601-4505800 204 +
chr11 4505701 4505900 chr11:4505701-4505900 241 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 612 +
chr11 4505601 4505800 chr11:4505601-4505800 279 +
chr11 4505701 4505900 chr11:4505701-4505900 217 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.raw.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 714 +
chr11 4505601 4505800 chr11:4505601-4505800 395 +
chr11 4505701 4505900 chr11:4505701-4505900 291 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Input.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 662.965 +
chr11 4505601 4505800 chr11:4505601-4505800 494.493 +
chr11 4505701 4505900 chr11:4505701-4505900 370.779 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Input.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 597.041 +
chr11 4505601 4505800 chr11:4505601-4505800 510.172 +
chr11 4505701 4505900 chr11:4505701-4505900 424.775 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Input.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 576.897 +
chr11 4505601 4505800 chr11:4505601-4505800 479.589 +
chr11 4505701 4505900 chr11:4505701-4505900 359.692 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Input.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 776.291 +
chr11 4505601 4505800 chr11:4505601-4505800 513.859 +
chr11 4505701 4505900 chr11:4505701-4505900 379.257 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Input.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 701.630 +
chr11 4505601 4505800 chr11:4505601-4505800 474.354 +
chr11 4505701 4505900 chr11:4505701-4505900 319.392 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Log2FC.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 0.450 +
chr11 4505601 4505800 chr11:4505601-4505800 -0.195 +
chr11 4505701 4505900 chr11:4505701-4505900 -0.055 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Output.mean.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 905.937 +
chr11 4505601 4505800 chr11:4505601-4505800 432.059 +
chr11 4505701 4505900 chr11:4505701-4505900 356.831 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Output.rep1.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 791.765 +
chr11 4505601 4505800 chr11:4505601-4505800 508.552 +
chr11 4505701 4505900 chr11:4505701-4505900 373.102 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Output.rep2.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 999.076 +
chr11 4505601 4505800 chr11:4505601-4505800 306.483 +
chr11 4505701 4505900 chr11:4505701-4505900 362.071 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Output.rep3.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 1035.589 +
chr11 4505601 4505800 chr11:4505601-4505800 472.107 +
chr11 4505701 4505900 chr11:4505701-4505900 367.194 + 

++++++++++++++++++++++++++++++++++++++++++
Save bed file: TMPRA_K562_OL45_20220927.hg38.norm.Output.rep4.stranded_pos.bed.gz
Chrom ChromStart ChromEnd Name Score Strand
chr11 4505501 4505700 chr11:4505501-4505700 797.319 +
chr11 4505601 4505800 chr11:4505601-4505800 441.094 +
chr11 4505701 4505900 chr11:4505701-4505900 324.958 +