User: jared.andrews07

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jared.andrews073.4k
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Ph.D. candidate at Washington University in St. Louis. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user, fledgling developer, hater of Perl. 

Posts by jared.andrews07

<prev • 423 results • page 1 of 43 • next >
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Comment: C: Segmentation fault (core dumped) #augustus
... You consider monitoring the memory usage of the program via `top` (or other methods) to see how much memory it's using while actually running. ...
written 4 days ago by jared.andrews073.4k
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Answer: C: how to normalize and compare CNV value in different samples
... You could try [CNVkit](https://cnvkit.readthedocs.io/en/stable/quickstart.html). It uses your normals to create a reference to which it'll compare each of your tumors. It's pretty quick and easy to use, so might at least be worth a shot for your case. Certainly easier than trying to do all the norma ...
written 4 days ago by jared.andrews073.4k
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Comment: C: CNV panel making
... What do you mean they don't match? Your setup and ultimate goal(s) are unclear, which make it difficult to provide any advice. ...
written 5 days ago by jared.andrews073.4k
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Answer: A: How many runs, samples, and studies are in the Sequence Read Archive?
... The first can be found [here](https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies), the second [here](https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=samples), and the third is...somewhere else. Can't help you there, I couldn't find it. ...
written 6 days ago by jared.andrews073.4k
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Comment: C: Combining two VCFs each with own set of mutations
... That's fine, it can still merge them and will even help you determine which caller called which variant (or where they overlap). ...
written 6 days ago by jared.andrews073.4k
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Answer: A: Clustering resolution single-cell RNA-seq
... Personally, I would likely merge the samples from the all donors (optionally performing integration if it appears there are donor effects) first. Clustering is going to pull out differences no matter what, even if they're quite minor. In cases such as this, you need to utilize your biological expert ...
written 6 days ago by jared.andrews073.4k
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Answer: A: Combining two VCFs each with own set of mutations
... [bcftools `merge`](https://samtools.github.io/bcftools/bcftools.html) is likely what you want. It will preserve the VCF format and genotype information for each sample appropriately. ...
written 6 days ago by jared.andrews073.4k
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Comment: C: Harmony batch correction vs. regressing out donor effect in Seurat
... The authors don't recommend it, as it's only meant to remove minor variation/biases due to differences in cell cycle, reads in mitochondrial genes, etc. rather than batch effects that affect every cell in a much more systemic manner. Their docs are a bit of a mess, so I can't find a specific referen ...
written 11 days ago by jared.andrews073.4k
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Answer: A: Harmony batch correction vs. regressing out donor effect in Seurat
... You should not use SCTransform to regress out batch effects. Rather, you should use one of [Seurat's integration methods](https://satijalab.org/seurat/v3.1/integration.html). Seurat also has a [number of wrappers](https://satijalab.org/seurat/vignettes.html#seurat-wrappers) around different integrat ...
written 11 days ago by jared.andrews073.4k
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Comment: C: It's there any GISTIC2.0 like tools?
... It *kind of* does that. It basically finds the recurrent CNVs between samples and tries to tie them back to which genes are affected. ...
written 12 days ago by jared.andrews073.4k

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