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My group is planning the WGS of a wild animal with a large genome size (approximately 6.5 Gb).
After the HiFi assembly, we plan to gap-close using Tell-seq reads and CLRs.
Due to budgetary constra…
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Hi, TengGao@teng-gao,
I am very interested in your research, but I have encountered some problems. I wonder if it is possible to run numbat with just the gene expression matrix and no allele file?I w…
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Hi there! We are currently using vcfdist for comparing variant callers. Our true set consists of 54 SNPs and 3 InDels (all of them homozygous). They seem to be picked up correctly as seen in the comma…
sq101 updated
6 months ago
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Snakemake 7.8 changes its rerun behavior. Before, rerunning jobs relied purely on file modification times.
Now, also provenance information is considered, like parameter changes, code changes, softwa…
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Hi all,
Thanks for the tool! I have a few questions
1) Are the _alt and _random files from the hg38 genome used as part of the search with the standard VCF sets? If so, can you explain how the…
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My 2d-SFS all have a blip at p=0.5 (see attached), which I assume is caused by lumped paralogs problem (i.e., SNPs that always appear as heterozygotes). Use HWE filter, you say - but I cannot filter t…
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Hello, @zengxiaofei
Can HapHiC input porec data? If not, what adjustments do I need to make?
Thank you in advance for your response
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Hello, I'm seeking clarification on the new `haplotagphase` command. The command is described as phasing a vcf file using haplotagged BAM/CRAM files. However, the CLI docstring specifies that the BAM/…
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Hello,
Thanks for making this tool accessible, really looking forward to trying it out on my nanopore data. I was wondering if you could help me figure out whether I have installed it properly or n…
smf96 updated
3 years ago
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I have a set of ~400bp amplicon ONT reads that were sequenced from a mixture of 700 closely related strains of one bacterial species. I'd like to run some error correction to reduce the errors in the …