Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
Reputation:
19,200
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
1 day, 17 hours ago
Joined:
8 years, 1 month 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 • 1,032 results • page 2 of 104 • next >
0
votes
4
answers
196
views
4
answers
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 10 weeks ago by Chris Miller19k
0
votes
2
answers
2.3k
views
2
answers
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 10 weeks ago by Chris Miller19k
2
votes
4
answers
303
views
4
answers
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 10 weeks ago by Chris Miller19k
1
vote
3
answers
324
views
3
answers
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 11 weeks ago by Chris Miller19k
2
votes
3
answers
324
views
3
answers
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 11 weeks ago by Chris Miller19k
0
votes
1
answer
166
views
1
answers
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 11 weeks ago by Chris Miller19k
0
votes
1
answer
301
views
1
answers
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 12 weeks ago by Chris Miller19k
2
votes
2
answers
252
views
2
answers
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 3 months ago by Chris Miller19k
0
votes
0
answers
26
views
0
answers
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 3 months ago by Chris Miller19k
3
votes
1
answer
328
views
1
answers
Answer: A: R package information
... Have you tried the instructions here to install from github (found on the first page of google results)? https://github.com/jtleek/genstats/issues/5 source("http://bioconductor.org/biocLite.R") biocLite("devtools") # only if devtools not yet installed devtools::install_github('RSkittl ...
written 3 months ago by Chris Miller19k

Latest awards to Chris Miller

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 4 months ago, created more than 1,000 posts (questions + answers + comments).
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
Scholar 5 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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why Should I Use Galaxy ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Popular Question 8 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1785 users visited in the last hour