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I tried running `alt_frac` and `coverage` scoring methods on the same inputs. Then I calculated the VAF based on alt and ref reads from the `coverage` output matrices. Most of the values agree, but so…
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This means that yane learns to simulate the training data or even games during training, which allows it to learn much faster in the scenario where only one genome can be trained at a time. Or if it i…
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Hi There,
I used the HiFi reads (~20x) to assemble a genome of an animal species. The output assembly is of high quality with N50 of 30 Mb. However, the genome size (2.6 G) is a bit larger than what …
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Hi, I have a problem when I convert my gtf file to + strand file. I do not what length I should enter. Total length of reference gene or whole length of genome. Because my gtf file is download for who…
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Hi, thanks for your useful tool to construct the genome 3D model. And I can run it using example data which named k562_1mb.txt under the sample_data folder, but when I use my own data, it happened no…
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In the Nature paper Computational 3D genome modeling using Chrom3D, the directory containing the Hi-C data from Rao et al and lamin ChIP-seq data from Lund et al is unobtainable because the link is br…
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When opening: https://genome.ucsc.edu/cgi-bin/hgPhyloPlace?db=wuhCor1&phyloPlaceTree=hgPhyloPlaceData/wuhCor1/public.plusGisaid.latest.masked.pb&subtreeSize=5000&remoteFile=https%3A%2F%2Flapis.cov-spe…
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Hi,
Can you explain what is the difference between the different variant ids? I don't see any documentation about this. For example, here are the most common variant types I found in one particul…
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I know this error has been resolved in other posts, but those solutions did not work for me. This is the output that I am getting:
mkdir: cannot create directory '7321.1.67340.GGTAGC.fastq': File e…
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Hi,
I'm currently trying to use 3d-dna (version 180922) to assemble a bird genome. The run-asm-pipeline.sh pipeline ran and generate almost all the .hic files except split stage. And, I got the follo…