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how to install Juicer hi-c
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11 months ago
dimitrischat • 60

https://github.com/aidenlab/juicer

Some help on how to install this software on ubuntu. I downloaded it run through terminal but i get this error :

"/opt/juicer/restriction_sites/hg19_MboI.txt does not exist. It must be created before running this script."

Where do i find this file ?

Is there an easier way i can install the program so everything is made automatically?

thanks

ChIP-Seq • 374 views
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Follow the Wiki which is even linked on the page you linked.

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thanks but the problem was that the script was looking for that file in some other place different than the "installation" folder which was weird. but that is fixed

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10 months ago
EagleEye 6.4k
Sweden

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 :)

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wow, thank you so much for the help. But i think (?) i did it with these steps :

cd /home mkdir references; cd references wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa mkdir ../restriction_sites; cd ../restriction_sites wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/restriction_sites/hg19_MboI.txt cd .. git clone https://github.com/theaidenlab/juicer.git ln -s juicer/SLURM/scripts/ scripts cd scripts wget http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicer/juicer_tools.1.7.6_jcuda.0.8.jar ln -s juicer_tools.1.7.6_jcuda.0.8.jar juicer_tools.jar cd .. mkdir HIC003; cd HIC003 mkdir fastq; cd fastq wget http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz wget http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz cd .. /home/scripts/juicer.sh -D /home

But still, when i run the script ./juicer.sh , it returns a problem " /opt/juicer/restriction_sites/hg19_MboI.txt does not exist. It must be created before running this script. "

While i have this file in the folder that i created in my /home/app/Desktop/apps/Juicer/restriction_sites

For some reason it tries to run it from opt/

Any idea why? ( i hope i described everything fine )

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Ideally it should not be a problem but try this,

Edit the script '/home/app/Desktop/apps/Juicer/CPU/juicer.sh'

juiceDir="/opt/juicer"

change to

juiceDir="/home/app/Desktop/apps/Juicer/"
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thanks a lot. that did the trick. now it appears to have another problem. "awk: cannot open /home/app/Desktop/apps/Juicer//scripts/common/chimeric_blacklist.awk (No such file or directory)"

edit: so i downloaded the file using this in chrome : # Core Juicer scripts from github in chrome : https://s3.amazonaws.com/juicerawsmirror/opt/juicer/scripts/chimeric_blacklist.awk

so i need all core juicer scripts? ( https://github.com/aidenlab/juicer/wiki/Installation )

edit2: new problem in terminal using the script : awk: /home/app/Desktop/apps/Juicer//scripts/common/chimeric_blacklist.awk: line 503: function and never defined

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