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Comment: How to Calulate Allele Frequency from a VCF File?
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Comment: How to Calulate Allele Frequency from a VCF File?
by
Emoji
• 0
Thanks, but how do i do that?
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Yes, you can use a reference genome from a related species to assemble transcripts of a target species. This approach is known as ```de nov…
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any tree is a valid hypothesis
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Hello Mensur, Could you look at my case too? interruption issue but a different error. This is the second time I face and I rerun it. I ha…
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my convergence value at 23 million run for last 10 days was at .017623 something. out of 7 million more remaining.
Comment: How to calculate Minion run time needed?
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andres.firrincieli
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> Does someone know how to calculate how many hours (approximately) i > need to run an minion, to get a good coverage for example of bacter…
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The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
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sanaz
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head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
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fuellen
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Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM
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Mike Smith
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Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
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congliu37
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Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
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I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
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Rob
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
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> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
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