Moderator: Chris Miller
Chris Miller ♦ 20k
- Reputation:
- 19,800
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- 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.
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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 Miller ♦ 20k
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12 follow
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... 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 ...
written 13 days ago by
Chris Miller ♦ 20k
• updated
12 days ago by
zx8754 ♦ 5.3k
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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 Miller ♦ 20k
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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 Miller ♦ 20k
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... 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 Miller ♦ 20k
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... 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 Miller ♦ 20k
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... 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 Miller ♦ 20k
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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 Miller ♦ 20k
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... 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 Miller ♦ 20k
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... 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 Miller ♦ 20k
Latest awards to Chris Miller
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12 days ago,
asked a question with at least 3 up-votes.
For Importing A Large Number Of References From Text
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For C: Should Biostar Be Switched Over To The Stackexchange Network?
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20 days ago,
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For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
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For A: Spliting a dataframe based in a chromosome
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For C: Should Biostar Be Switched Over To The Stackexchange Network?
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3 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
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5 months ago,
created a question with more than 1,000 views.
For Efficiently storing methylation data from BS-sequencing
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created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
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For C: All Possible Substitutions In The Human Reference Genome
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created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
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7 months ago,
created an answer that was upvoted at least 5 times.
For A: Should I Remove The Unmapped Reads From My Bam ?
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?
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
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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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