Moderator: Chris Miller
Chris Miller ♦ 19k
- 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.
0
votes
4
answers
196
views
4
answers
... Try the GATK `LeftAlignAndTrimVariants` tool, which will at least normalize their positions and help improve concordance. ...
written 10 weeks ago by
Chris Miller ♦ 19k
0
votes
2
answers
2.3k
views
2
answers
... 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 Miller ♦ 19k
2
votes
4
answers
303
views
4
answers
... 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 Miller ♦ 19k
1
vote
3
answers
324
views
3
answers
... 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 Miller ♦ 19k
2
votes
3
answers
324
views
3
answers
... 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 Miller ♦ 19k
0
votes
1
answer
166
views
1
answers
... 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 Miller ♦ 19k
0
votes
1
answer
301
views
1
answers
... 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 Miller ♦ 19k
2
votes
2
answers
252
views
2
answers
... 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 Miller ♦ 19k
0
votes
0
answers
26
views
0
answers
... 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 Miller ♦ 19k
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 Miller ♦ 19k
Latest awards to Chris Miller
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 ?
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?
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
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?
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
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
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