Moderator: Chris Miller
Chris Miller ♦ 18k
- Reputation:
- 18,010
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://www.chrisamille...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 10 hours ago
- Joined:
- 7 years, 4 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.
2
votes
1
answer
138
views
1
answers
... In almost all cases cases, each TCGA patient only had tumor RNAseq done. ([see previous discussions][1]). Are you sure that there was actually normal RNAseq available, or have you pulled down the same file twice through different linkages?
[1]: https://www.biostars.org/p/179681/#179746 ...
written 5 weeks ago by
Chris Miller ♦ 18k
0
votes
0
answers
82
views
0
answers
Comment:
C: TCGA AML data set analysis
... Most TCGA samples do not have matched normal RNAseq. See previous questions like this for details: https://www.biostars.org/p/179681/#179746. If you have more questions about RNAseq that have not already been answered, feel free to ask a new question. ...
written 5 weeks ago by
Chris Miller ♦ 18k
1
vote
3
answers
153
views
3
answers
... bam-readcount does this: https://github.com/genome/bam-readcount ...
written 6 weeks ago by
Chris Miller ♦ 18k
0
votes
3
answers
514
views
3
answers
... I can't tell from what you've provided what the issue is (and since the code is so old, I don't remember the details either). You'll probably have to step through the script step by step to figure out what's going on. I'd start by making sure that the outputs created by the previous steps in runEach ...
written 6 weeks ago by
Chris Miller ♦ 18k
0
votes
0
answers
95
views
0
answers
... You're going to have to teach yourself some basic unix skills or get help from a sysadmin. There are many resources available on the internet for doing the former. Best of luck ...
written 6 weeks ago by
Chris Miller ♦ 18k
0
votes
1
answer
217
views
1
answers
Answer:
A: SciClone on WES data
... [1] "checking input data..."
[1] "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2."
can't do clustering - no copy number 2 regions to operate on in sample 1
This error means that every mutation in your sample falls eithe ...
written 6 weeks ago by
Chris Miller ♦ 18k
0
votes
2
answers
148
views
2
answers
... Without more information, I'm afraid that I can't help you. The scripts provided are short and straightforward. Your error relates to not being able to find specific files that it expects to be there. Make sure all preceding steps have completed successfully. If you go line by line through the proce ...
written 6 weeks ago by
Chris Miller ♦ 18k
0
votes
1
answer
218
views
1
answers
... VAF = variant allele frequency, expressed as a percentage between 0 and 100.
The most typical use case for Regions to exclude is the case of copy number neutral loss of heterozygosity: that is, an area that has copy number 2 but has the same alleles twice due to uniparental disomy. ...
written 10 weeks ago by
Chris Miller ♦ 18k
1
vote
2
answers
177
views
2
answers
... Update - this doesn't seem to happen on my laptop's more recent install of VEP (version 87 vs version 86). I guess it's either a version issue or a somehow screwy install. I'm going to go ahead and mark this as the best answer for now, as an upgrade seems like it will solve the problem.
If anyone ...
written 11 weeks ago by
Chris Miller ♦ 18k
0
votes
2
answers
177
views
2
answers
... Sadly, that's not the issue. I'm editing the post above to make the VCF even simpler and make the FORMAT lines match up 100% with the fields - the same warning and header recognition issue persists. ...
written 11 weeks ago by
Chris Miller ♦ 18k
Latest awards to Chris Miller
Appreciated
15 days ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Epic Question
4 weeks ago,
created a question with more than 10,000 views.
For Bioinformatics "Cheat Sheet"
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Exon Array Analysis Tools
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Exon Array Analysis Tools
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For Exon Array Analysis Tools
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Good Answer
3 months ago,
created an answer that was upvoted at least 5 times.
For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Importing A Large Number Of References From Text
Scholar
5 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Appreciated
5 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated
6 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: Aligning Reads To Specific Chromosome Using Bwa
Appreciated
7 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 464 users visited in the last hour