Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
19,800
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
7 hours ago
Joined:
8 years, 7 months ago
Email:
c***********@gmail.com

I work in the Division of Oncology and McDonnell Genome Institute at Washington University in St. Louis, where I develop and apply computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,067 results • page 2 of 107 • next >
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Comment: C: Code Golf - bisulfite conversion
... This is correct, it's either C->T or G->A, but not both! ...
written 12 days ago by Chris Miller20k
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Code Golf - bisulfite conversion
... Been a while since we had a code golf challenge (shortest script wins, but expect to receive upvotes for cleverness)! Simplifying slightly, bisulfite conversion means that Cs get converted to Ts, but some bases may be protected by methylgroups and thus remain unconverted. (This happens on the opp ...
codegolf bsseq forum bisulfite golf written 13 days ago by Chris Miller20k • updated 12 days ago by zx87545.3k
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Comment: C: Fishplot R package
... Hi, fishplot creator here. Jared's advice is sound - start there. If you have continued issues, feel free to follow up here or post an issue on the github page ...
written 27 days ago by Chris Miller20k
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Comment: C: bam-readcount core dump
... The most common reason for bam-readcount crashes/core dumps are a mismatch between reference fasta and bam file. Are you sure that none of of your reads goes past the end of the chromosome sizes defined in your fasta? ...
written 10 weeks ago by Chris Miller20k
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Answer: A: high frequency SNPs (and other variations) after subtracting blood variants from
... If you're trying to call somatic variants, you should use a somatic variant caller (Such as Mutect, Strelka, or VarScan). The results will be different than if you simply compare tumor SNPs to normal SNPs, as there are statistical assumptions that are very different between the two models. ...
written 3 months ago by Chris Miller20k
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Answer: A: Should bioinformaticians learn the scientific names of plants and animals?
... Almost certainly no. Beyond "Homo sapiens" and "Mus Musculus", there are probably only two or three I'd recognize. You'll pick up domain specific knowledge like that by diffusion from whatever project you're on, but a calculated study of them is probably not a good use of your time. ...
written 3 months ago by Chris Miller20k
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Answer: A: How to distinguish methylated cytosine and unmethylathed cytosine?
... You've just answered your own question. At each C/T in the genome, you'll see a mix of methylated (preserved base) and unmethylated (changed base) reads. The methylation fraction for a site is the methylated count over the total reads at that base. ...
written 3 months ago by Chris Miller20k
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Answer: A: Neoantigen prediction Tools
... I've helped to develop [pVACtools](https://github.com/griffithlab/pVACtools) along with some very talented people from the Griffith lab here at WUSTL. It works well [Vaxrank](https://www.biorxiv.org/content/early/2017/05/27/142919) is another, from the Hammerbacher lab ...
written 3 months ago by Chris Miller20k
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Comment: C: Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
... Yes. In most cases, the probes or regions are small enough, that treating them as point estimates is fine. ...
written 4 months ago by Chris Miller20k
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Answer: A: Clonal evolution for samples with no common CNV
... You're going to have to provide more information, starting with exactly what the error message was. I strongly suspect that the message was "ERROR: no sites are copy number neutral and have adequate depth in all samples", which means you need to look at your inputs carefully. Did your points meet ...
written 4 months ago by Chris Miller20k

Latest awards to Chris Miller

Student 12 days ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 12 days ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 12 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 5 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 10 months ago, created more than 1,000 posts (questions + answers + comments).
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Appreciated 10 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 10 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 11 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome

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