DpnII in calculate-snv

[malonzm1]

Hi, In scripts/calculate-snv, the weblinks contain 'hg38.DpnII.npz': 'http://3dgenome.fsm.northwestern.edu/neoLoopFinder/hg38.MboI.npz'. Shouldn't this be hg38.DpnII.npz? Thanks.

[malonzm1]

Also, is there a way I can modify the conda scripts so that calculate-cnv doesn't download files (I will just copy them because our server doesn't have internet)?

[XiaoTaoWang]

1. DpnII and MboI recognize exactly the same cutting sites, which is why they share the same link.
2. To run calculate-cnv offline, you can create a folder named .cache in your working directory (the directory where you plan to submit your job). Then, download the these reference genome data to your laptop and upload them to the .cache folder.

[malonzm1]

Thanks!

Btw, I generated a loop output file using neoloop but there were very loops found. Any ideas? The following commands were used (from pairs output file from HiCool)

cooler cload pairs -c1 2 -p1 3 -p2 4 -c2 5 ~/utilities/ucsc/hg38.chrom.sizes:5000 temp.pairs temp.cool

cooler zoomify --nproc 4 --resolutions 5000,10000,25000,50000,100000,250000,500000,1000000,2500000,5000000 --balance --balance-args "--min-nnz 10 --mad-max 5" -o temp.mcool temp.cool
calculate-cnv -H temp.mcool::/resolutions/10000 -g hg38 -e DpnII --output temp.bedGraph
segment-cnv --cnv-file temp.bedGraph --output temp-seg.bedGraph --binsize 10000 --nproc 4 --ploidy 2
cooler balance temp.mcool::/resolutions/10000

mamba activate EagleC
predictSV --hic-5k temp.mcool::/resolutions/5000 \
            --hic-10k temp.mcool::/resolutions/10000 \
            --hic-50k temp.mcool::/resolutions/50000 \
            -O temp -g hg38 --balance-type ICE --output-format NeoLoopFinder \
            --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999

conda deactivate

correct-cnv -H temp.mcool::/resolutions/10000 --cnv-file temp-seg.bedGraph --nproc 4

assemble-complexSVs -O temp -B temp.CNN_SVs.5K_combined.txt --balance-type ICE --protocol insitu --nproc 4 -H temp.mcool::resolutions/10000

neoloop-caller -O temp.neo-loops.txt --assembly temp.assemblies.txt --balance-type ICE --protocol insitu --prob 0.95 --nproc 4 -H temp.mcool::resolutions/10000