# Download from UCSC like so:
# wget ftp://hgdownload.cse.ucsc.edu/gbdb/hg38/bbi/wgEncodeReg/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig /mnt/bigData2/andrew/histoneENCODE/
# Convert from bigWig to wiggle like so:
# andrew@smirnov:~/Qual/UCSCscripts$ ~/Qual/UCSCscripts/bigWigToWig /mnt/bigData2/andrew/histonENCODE/bigWigs/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig ~/Qual/data/wiggles/wgEncodeBroadHistoneK562H3k27acStdSig.wiggle
# Remove the hashmark lines from the wiggle like so
#grep -v '^#' ~/Qual/data/wiggles/wgEncodeBroadHistoneK562H3k27acStdSig.wiggle > ~/Qual/data/wigglesNoHashes/wgEncodeBroadHistoneK562H3k27acStdSigNoHashes.wiggle
library(readr)
library(dplyr)
library(magrittr)
library(ggplot2)
library(stringr)
# k562H3k27 = read_tsv('~/Qual/data/wigglesNoHashes/wgEncodeBroadHistoneK562H3k27acStdSigNoHashes.wiggle',
# col_names = c('chr', 'start', 'stop', 'value'))
#
# testRegion = k562H3k27 %>%
# filter(chr == 'chr7',
# start > 80750000, #A region that's ~200kb downstream of CD36, just picked it out because it had a couple peaks
# stop < 80900000) %>%
# mutate(mids = (start + stop)/2,
# widths = (stop - start))
#
# ggplot(testRegion, aes(mids, value)) +
# geom_col(width = testRegion$widths)
####Okay this lines up with the data visible on the UCSC browser so let's just download every histone mark dataset
fileNames = system('grep K562H[0-9]k[0-9] /mnt/bigData2/andrew/histoneENCODE/Index\\ of\\ _goldenPath_hg19_database.html', intern = TRUE) %>%
grep('.txt.gz', ., value = TRUE) %>%
grep('Sig', ., value = TRUE)
fileStarts = fileNames %>% str_locate(., 'wg') %>% .[,1]
fileStops = (fileNames %>% str_locate(., '.txt.gz') %>% .[,1]) - 1
files = fileNames %>% str_sub(., start = fileStarts, end = fileStops)
save(files, file = '~/Qual/data/histoneMarkFileNames.RData')
#download each bigWig
setwd('/mnt/bigData2/andrew/histoneENCODE/bigWigs/')
for(i in 1:length(files)){
download.file(paste0('ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/', files[i], '.bigWig'), destfile = paste0(files[i], '.bigWig'), quiet = TRUE)
}
# bigWigToWig each file
setwd('/mnt/bigData2/andrew/histoneENCODE/wiggles/')
for(x in 1:length(files)){
system(paste0('~/Qual/UCSCscripts/bigWigToWig ',
'/mnt/bigData2/andrew/histoneENCODE/bigWigs/', files[x], '.bigWig ',
files[x], '.wiggle'))
}
#remove hashmark lines from each wiggle
for(x in 1:length(files)){
system(paste0('grep -v ^# ',
files[x], '.wiggle > temp && mv temp ',
files[x], '.wiggle'))
}
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