User: Grey Monroe

gravatar for Grey Monroe
Grey Monroe10
Reputation:
10
Status:
New User
Location:
Max Planck Institute
Website:
https://www.monroelab....
Twitter:
grey_monroe
Scholar ID:
Google Scholar Page
Last seen:
3 months, 2 weeks ago
Joined:
5 years, 10 months ago
Email:
g*********@gmail.com

Post doc at Max Planck Institute for Developmental Biology

Posts by Grey Monroe

<prev • 13 results • page 1 of 2 • next >
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Comment: C: SnpEff START/STOP codon not found error
... Thomas, Any progress figuring this out? I have same errors with different species. IGV looks fine. ...
written 8 months ago by Grey Monroe10
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Comment: C: fastest UMAP method
... Any idea why (where df = 30000row*36col dataframe) umap(df, n_components= 2, n_neighbors=200, min_dist=0.25) would produce Error: vector memory exhausted (limit reached?) Lower n_neighbors values do not yield this error. ...
written 9 months ago by Grey Monroe10
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Comment: C: filter vcf to include only sites which have at least one homozygous alt call
... Works perfect thank you ...
written 9 months ago by Grey Monroe10
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filter vcf to include only sites which have at least one homozygous alt call
... Hi all, I am trying to extract a subset of sites from a multi-sample vcf file. I only want those sites with at least one homozygous alternative allele call. Some sites are poly-allelic so sites that I want would have at least one 1/1 or 2/2 call. I've looked through bcftools, vcftools, but haven't ...
vcf written 9 months ago by Grey Monroe10 • updated 9 months ago by finswimmer13k
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Comment: C: fastest UMAP method
... Thank you for the great suggestions! ...
written 9 months ago by Grey Monroe10
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Comment: C: fastest UMAP method
... Good question. Prohibitive only for exploratory analyses (hours). I'd like to see how the output changes with adjustments to parameters like number of neighbors. ...
written 9 months ago by Grey Monroe10
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fastest UMAP method
... I am trying to generate a Uniform Manifold Approximation and Projection (UMAP) for about 300,000 observations of 36 variables. So far I have been using the *umap* package in R but this seems prohibitively slow (for exploratory analyses and parameter optimisation). Can someone recommend an alternativ ...
R umap written 9 months ago by Grey Monroe10
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blastp augustus annotation against protein database
... Hi all. I'm looking for a handy tool to blast amino acid sequence output from Augustus annotation against a protein database to identify the best ortholog. I can imagine doing this with a homemade script but thought there might be a ready made tool out there. Thanks in advance! Details: Augustus ...
augustus annotation blast written 9 months ago by Grey Monroe10 • updated 9 months ago by lieven.sterck8.2k
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Comment: C: Predicting coding sequence region from GFF with exons + reference genome
... > do a prediction What do you mean? Does it find a CDS that makes sense (ie starts with start codon and ends with stop codon?) ...
written 9 months ago by Grey Monroe10
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Comment: C: ways to improve SnpEff prediction
... > the prediction seems to gave inaccurate number of effects in ann.vcf file. Can you elaborate in more detail? ...
written 9 months ago by Grey Monroe10

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