Final exam - areed37/Andrew_Reed_EPP_531 GitHub Wiki

Genome assembly with redbud

My part 1/2 (scaffolding)

mkdir Juicer
cd Juicer/

#Hap 1
mkdir hap1
cd hap1/

mkdir references
cd references/
ln -s </pwd/hap1.p_ctg.fasta> .

spack load /be6uuqp
bwa index hap1.p_ctg.fasta
cd ..

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 ..

mkdir fastq
cd fastq/
ln -s /path_to/salbidum01_1334141_S3HiC_R1.fastq.gz .
ln -s /path_to/salbidum01_1334141_S3HiC_R2.fastq.gz .
cd ..

bash /pickett_shared/software/juicer-1.6/CPU/juicer.sh \
        -g sassafrass_hap1.p_ctg \
        -D /pickett_shared/software/juicer-1.6/CPU/ \
        -t 10 \
        -d /path_to/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

My part 2/2