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Hello,
I am currently working on scaffolding an F1 hybrid genome, which has 55 chromosomes per haplotype: 27 chromosomes from parental species 1 and 28 from parental species 2. I am using HiFi / H…
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I am trying to create 3D genome model for full genome but Chrom3D is taking forever to complete. 81+ hrs since job submission. And i have noticed that it is running on a single thread. Is there a way …
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Hello,
I would like to express my gratitude for developing such a lightweight tool. I believe that data format conversion is a common issue in three-dimensional genome research and I would like to …
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1) export godot to playground
2) load playground
3) load any genome (I used essential essence)
4) See that everything include 3D indicator erased
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Hi,
Thanks for developing this tool, i was trying to run this pipeline, i run juicer pipeline with my draft geneme first, then i used "merged_nodups.txt" for puzzle, I got an issue when doing the 9th…
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Dear 3D-DNA users,
I used 3D-DNA to assemble a plant genome. the initial genome size was 1.6G, after using 3D-DNA pipeline it became 1.4G. I want to know why this happened and where is the 0.3G data?…
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We are working on genome assembly of an interspecific hybrid plant having two genomes.
During the 3d-dna step even with haploid mode and diploid, we always had errors saying:
> :( Assembly file …
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Hi ,
I ran 3d-dna for a plant genome with the command:
sh 3d-dna/run-asm-pipeline.sh 9201_Genome_Scaffold.fasta merged_nodups.txt
I got error infomation as follows:
awk: 3d-dna-master/util…
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hello my friends
when adjuest the juicerbox, geneated the review.assembly . and use the run-asm-pipeline-post-review.sh to genearate the final fasta ,but its error. my genome size was 23g, and the fi…
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Hello~ This is a wonderful tool for people who are in the field~!
I already have the final outputs of HiCPro (such as .matrix and _abs.bed ), I don't need to run HiCPro again through 3d-genome-buil…