3D‐DNA and Interacting with Hi‐C - Lavadav/EPP531_AGA GitHub Wiki

10. 3D-DNA

Create new folder

mkdir 3D-DNA
cd 3D-DNA

Link the Fasta and Juicer output.

ln -s Path_to/Juicer/aligned/merged_nodups.txt .
ln -s Path_to/Juicer/references/*fasta .

Load Parallel

spack load /acgsl7y

Run 3D-DNA

bash /pickett_shared/software/3d-dna-201008/run-asm-pipeline.sh Your_Assembly.fasta merged_nodups.txt

or

bash /pickett_shared/software/3d-dna-201008/run-asm-pipeline.sh --editor-repeat-coverage 8 --editor-coarse-resolution 50000 --editor-coarse-region 250000 Your_Assembly.fasta merged_nodups.txt

Finalize 3D-DNA

bash /pickett_shared/software/3d-dna-201008/finalize/finalize-output-w-stats.sh \
        -c 12 \ #no. of chromosomes
        -s 15000 \ #tiny_thresholds
        -l Your_Assembly \
        Your_Assembly.final.cprops \
        Your_Assembly.final.asm \
        Your_Assembly.final.fasta \
        final \
        >& Your_Assembly.3d_dna_final.out

Download Final .hic and .assembly files for Juicebox

Juicebox Documentation

https://github.com/aidenlab/Juicebox

Juicebox Tutorial

Optional Step (on case by case basis)

bash /pickett_shared/software/3d-dna-201008/run-asm-pipeline-post-review.sh -r \
Your_Assembly.final.review.assembly \
Your_Assembly.fasta \
merged_nodups.txt

11. Accessing Completeness

Run BUSCO on your new Genome Assembly

12. SyRi: Visualizing the genome

Make new directory

mkdir Syri
cd Syri

Link the fasta files in the current directory

ln -s /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/Syri/*.fa .

Align the two fasta sequences

spack load minimap2
minimap2 -ax asm5 -t 5 hap1_subset_9.fa hap1_subset_9.fa > hap1-vs-hap2.sam

convert SAM to BAM

spack load /r67sol
samtools view -b -@ 1 hap1-vs-hap2.sam > Dogwood_hap1-vs-hap2_Chr9.bam

## Delete the SAM file to save space

rm hap1-vs-hap2.sam

Running SyRi on BAM file

singularity exec -B $PWD /sphinx_local/images/syri_1.6.3--py38hdbdd923_2.sif syri -c Dogwood_hap1-vs-hap2_Chr9.bam -r hap1_subset_9.fa -q hap2_subset_9.fa -F B --cigar --nc 3

make a text file to name Fasta files

nano genomes.txt

"Genome.txt" file format

hap1_subset_9.fa        Hap1_Chr09
hap2_subset_9.fa        Hap2_Chr09

Plot Figure with plotsr

#Install plotsr with conda
conda create -n plotsr
conda activate plotsr
conda install bioconda::plotsr

#Run Plotsr
plotsr --sr syri.out --genomes genomes.txt -o ChBrave_chr9-vs-K2_chr9.png -H 8 -W 10 -d 300

conda deactivate