Hi,

I followed these steps to use hg38 restriction sites in juicer,

Step 1) Use 'findRestrictionSites.pl' from HiCUP pipeline.

Edit

my $chr_file = "/proj/uppstore2018034/santhilal/bin/juicer/Homo_sapiens.GRCh38.dna.chromosome.$chromosome".".fa.gz";

system("wget ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome."."$chromosome".".fa.gz");

Run as script

for i in `seq 1 22`;
do

perl findRestrictionSites.pl --genome_version=hg38 --chromosome=${i} --re_site=GATC | awk '{printf("MboI_site_1%d\t%s\n",NR,$0)}' | sed 's/\:/\t/g' | sed 's/\-/\t/g' | awk '{print $2"\t"$3"\t"$4"\t"$1;}' > /proj/uppstore2018034/santhilal/bin/juicer/MboI_restriction_sites/hg38_chr${i}_MboI.rmap ;

cat restriction_sites/hg38_chr${i}_MboI.rmap | cut -f1,2 | awk 'BEGIN{FS="\t"}{ if( !seen[$1]++ ) order[++oidx] = $1; stuff[$1] = stuff[$1] $2 " " } END { for( i = 1; i <= oidx; i++ ) print order[i]"\t"stuff[order[i]] }' | sed 's/\t/ /g' | sed 's/chr//g' > restriction_sites/hg38_chr${i}_MboI.txt ;


done

Step 2) Merge restriction sites from all chromosomes (in order)

cat restriction_sites/hg38_chr1_MboI.txt restriction_sites/hg38_chr2_MboI.txt restriction_sites/hg38_chr3_MboI.txt [....] restriction_sites/hg38_chr22_MboI.txt > restriction_sites/hg38_Mbol.txt

Step 3) Extract chromosome sizes to to add at the end of restriction sites file

cat references/hg38.fa.fai | cut -f1,2 | sort -g -k1,1 | sed 's/\t/ /g' > references/hg38.fa.fai.tmp

Step 4) Combine chromosome size with restriction sites file

join restriction_sites/hg38_MboI.txt.bak references/hg38.fa.fai.tmp > restriction_sites/hg38_MboI.txt

I hope this helps :)