Moderator: karl.stamm

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karl.stamm3.4k
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Posts by karl.stamm

<prev • 454 results • page 1 of 46 • next >
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Answer: A: Diploid calls on chrY?
... Some regions of chrY are duplicated on chrX, it's called the pseudo-autosomal region, because it appears to behave like autosomes. Wikipedia tells me that this location, 59megabases could be included . https://en.wikipedia.org/wiki/Pseudoautosomal_region ...
written 14 days ago by karl.stamm3.4k
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Comment: C: Diploid calls on chrY?
... Big chunks of Y are copied on X, so maybe this is the so-called pseudo-autosomal region? ...
written 14 days ago by karl.stamm3.4k
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Comment: C: Missing data in covariate file in PLINK
... I don't know what your .bim is, but you should be able to recode any file, or just run the software separately for each condition. I gather PLINK is just running one column of the phenotype file anyway, you'll be doing separate analyses. You're trying to do several analyses right now with incompat ...
written 25 days ago by karl.stamm3.4k
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Answer: A: Missing data in covariate file in PLINK
... PLINK v1.9 has a parameter --missing-phenotype which lets you assign a number other than -9 as the key for missing value. see their docs for encoding parameters https://www.cog-genomics.org/plink/1.9/input#pheno ...
written 26 days ago by karl.stamm3.4k
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Comment: C: Where can I find phage nucleotide sequences with lytic/lysogenic labels?
... You've asked an awful lot of questions. ...
written 27 days ago by karl.stamm3.4k
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Comment: C: How to multiply all the elements of the list together?
... I would use R, which has a built in function for it, prod(1:10) returns 10 factorial. Is this homework? It's probably going to be closed as not bioinformatics, and you should ask the general programming forums. It's not clear what youre trying to do, since the multiplyList() appears to work! ...
written 5 weeks ago by karl.stamm3.4k
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Comment: C: How to identify a species is autopolyploid or allopolyploid by high-throughput s
... define your terms please? sounds like an interesting problem, but I'm not familiar with the classes auto/allo polyploidy. A quick google looks like these phrases refer to the ancestry of the multi-copy genome in your sample. Do you know the ancestry of the mouse? It doesn't sound like something a t ...
written 6 weeks ago by karl.stamm3.4k
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Comment: C: Cluster samples based on expression of a subset of genes
... Take a look at bioconductor/rgsepd where I run DESeq to find genes with differences, then GOSeq to find gene groups of significance, then it moves on to what you're asking for directly. Subset the counts matrix by gene set, PCA on the sub-space, and youll get clustering with respect to named gene se ...
written 11 weeks ago by karl.stamm3.4k
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Comment: C: Why is 0/0 homozygous reference call in VCF useful information?
... I like to know the difference between "confident data we see hom-ref" and "no-data". Your single-sample VCF is only showing mutant sites, but I often run a VCF at a given set of coordinates, and I want to know which of the four situations is going on. 0/0 or 0/1 or 1/1 or no-data. ...
written 3 months ago by karl.stamm3.4k
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Comment: C: Neural networks feature importance
... Sorry I am not familiar with anything called Garson. So it's not clear what you mean by importances. I use least-squares optimization (minimize sum of squared differences) with customized endpoints, sometimes using what TensorFlow calls a softmax activation function. ...
written 4 months ago by karl.stamm3.4k

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Teacher 17 days ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
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Popular Question 10 months ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 2.9 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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