Scaffolding Contigs with Hi‐C - heelsplitter/Grootmyers_EPP_531_Applied_Genome_Analytics GitHub Wiki

Scaffolding Slides

9. Juicer

cd /pickett_sphinx/projects/EPP531_AGA/dgrootmy
mkdir Juicer
cd Juicer/

#Hap 1

mkdir hap1
cd hap1/

mkdir references
cd references/
source ~/.bashrc
ln -s /pickett_sphinx/projects/EPP531_AGA/Pokhrel/MT_CP_removal/assembly_finalfiltered.fasta .

spack load /be6uuqp
bwa index assembly_finalfiltered.fasta
cd ..

#Did not run this step personally
mkdir restriction_sites
cd restriction_sites/
python /pickett_shared/software/juicer-1.6/misc/generate_site_positions.py DpnII sassafrass_hap1.p_ctg ../references/sassafrass_hap1.p_ctg.fasta
awk 'BEGIN{OFS="\t"}{print $1, $NF}' sassafrass_hap1.p_ctg_DpnII.txt > sassafrass_hap1.p_ctg_DpnII.chrom.sizes
cd ..

#Did not run this step personally
mkdir fastq
cd fastq/
ln -s /pwd/salbidum01_1334141_S3HiC_R1.fastq.gz .
ln -s /pwd/salbidum01_1334141_S3HiC_R2.fastq.gz .
cd ..

#Did not run this step personally
bash /pickett_shared/software/juicer-1.6/AWS/scripts/juicer.sh \
        -g sassafrass_hap1.p_ctg \
        -D /pickett_shared/software/juicer-1.6/AWS/ \
        -t 10 \
        -d /pwd/Juicer/hap1/ \
        -z ./references/sassafrass_hap1.p_ctg.fasta \
        -p ./restriction_sites/sassafrass_hap1.p_ctg_DpnII.chrom.sizes \
        -y ./restriction_sites/sassafrass_hap1.p_ctg_DpnII.txt