Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
Reputation:
19,040
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
16 hours ago
Joined:
7 years, 11 months ago
Email:
c***********@gmail.com

I work in the Genome Institute at Washington University in St. Louis, where I lead a group that develops and applies computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,023 results • page 1 of 103 • next >
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Answer: A: Mapping Protein Mutation to Genomic DNA
... The short answer is you can't, because the amino acid code is degenerate. The long answer is, you can get close, if you're willing to make assumptions about the specific transcript being used and guess at which mutation caused a specific AA change, as there are several different possibilities. The ...
written 6 days ago by Chris Miller19k
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Answer: A: Indel concordance from different VCF files
... Try the GATK `LeftAlignAndTrimVariants` tool, which will at least normalize their positions and help improve concordance. ...
written 13 days ago by Chris Miller19k
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Comment: C: Problems After Loading Varscan 2 Output Into Bioconductor.Dnacopy
... without seeing any of your data, there's really no way to tell, but one thing that jumps out is that you've replaced as.numeric(cn[,6]) with as.numeric(cn[,7]) Are you sure you're extracting the right columns? ...
written 14 days ago by Chris Miller19k
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Answer: A: Saving IGV images for bigwig files
... You can do this with batch files in IGV. Here's a little wrapper script that automates some of it: https://github.com/chrisamiller/igvScreenshot To be clear, I know you said no screenshots, but on a headless node, you can expand these to whatever height/size you want by tweaking params. ...
written 18 days ago by Chris Miller19k
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Comment: C: Computer logistics of comparing genomes within same individual
... This seems quite analogous to the problem of identifying tumor-specific antigens. You might look at the ways in which that's implemented in immunotherapy pipelines (i.e http://pvactools.org) for some rough ideas. I still don't really understand your end goal, but I'd start by: 1) Identifying all c ...
written 19 days ago by Chris Miller19k
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Answer: A: Computer logistics of comparing genomes within same individual
... You want to be looking for how people detect either a) somatic mosaicism or b) tumor-specific (somatic) variants. There are a wealth of tools for doing this by setting one sample as the normal and comparing to find the changes in the other. From your description, it seems as though your method would ...
written 19 days ago by Chris Miller19k
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Answer: A: Does bisulfite sequencing need higher sequencing depth than regular genomic sequ
... It depends on your experimental design and what information you hope to retrieve. That said, if anything, lower coverage is needed. 2-3x gives reasonable results when you leverage the fact that the methylation of nearby CpGs are heavily correlated. 10x gives really nice CpG-level resolution across ...
written 24 days ago by Chris Miller19k
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Comment: C: tumor/normal WGS with CNVkit has many small segments with small copy number chan
... 1) Are the tumor and normal samples from the same rat? Or just from the same strain? There can be more heterogeneity than you expect sometimes. I'm still not sure whether that would explain that result, though... ...
written 26 days ago by Chris Miller19k
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Answer: A: ExAC includes WES of phenotyped population
... Sure - ExAC is useful for lots of things, but it is not designed to be a control for common disease studies. That requires sequencing a well-phenotyped cohort of individuals known to be negative for your trait of interest. ...
written 4 weeks ago by Chris Miller19k
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Comment: C: hey, can someone help me with python?
... Biostars is not a forum for providing homework answers. If this is not homework, and you've put together something that failed, then try another post that shows what you've tried and why it fails and we may be able to help point you in the right direction. Best of luck. ...
written 4 weeks ago by Chris Miller19k

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Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
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