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Question: how to install Juicer hi-c
0
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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

ADD COMMENTlink 13 months ago dimitrischat • 60
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1

Follow the Wiki which is even linked on the page you linked.

ADD REPLYlink 13 months ago
ATpoint
17k
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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

ADD REPLYlink 13 months ago
dimitrischat
• 60
2
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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 :)

ADD COMMENTlink 13 months ago EagleEye 6.4k
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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 )

ADD REPLYlink 13 months ago
dimitrischat
• 60
Entering edit mode
1

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/"
ADD REPLYlink 13 months ago
EagleEye
6.4k
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0

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

ADD REPLYlink 13 months ago
dimitrischat
• 60

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