Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
19,580
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
12 minutes ago
Joined:
8 years, 5 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 • 1,054 results • page 1 of 106 • next >
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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 14 days 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 4 weeks 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 5 weeks 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 7 weeks 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 7 weeks 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 10 weeks 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 11 weeks ago by Chris Miller20k
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Comment: C: Sciclone took too long
... Tumor only means that you will almost certainly not be able to remove all germline mutations. The isown paper will provide some useful guidelines for how you can minimize them though. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0446-9 ...
written 11 weeks ago by Chris Miller20k
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Comment: C: SciClone: Why cluster in non-CN neutral region considering it infers only on CN
... Yep, you've got it. Just look at the 2 copy plot for clustering. There's also an option to show just the CN2 regions in the plotting command. ...
written 11 weeks ago by Chris Miller20k
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Answer: A: SciClone: Why cluster in non-CN neutral region considering it infers only on CN
... > Then why do I see clusters on non-CN neutral region (1 copy and 3 copies)? They're plotted by default in a 1d view (in the appropriate row), but not utilized for clustering. I'd need more information on exactly what your inputs and outputs are to offer more help. ...
written 11 weeks ago by Chris Miller20k

Latest awards to Chris Miller

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 4 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 3 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 8 months ago, created more than 1,000 posts (questions + answers + comments).
Good Answer 8 months 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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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Appreciated 9 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Scholar 9 months ago, created an answer that has been accepted. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E

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