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
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