Moderator: Chris Miller
Chris Miller ♦ 20k
- Reputation:
- 20,040
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 59 minutes ago
- Joined:
- 8 years, 9 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: Google announces DeepVariant
... Mark isn't trying to hide that fact - consider your post the disclaimer! ...
written 9 weeks ago by
Chris Miller ♦ 20k
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Comment:
C: SciClone on WES data
... You can also just add the `cnCallsAreLog2=TRUE` param when running sciclone ...
written 9 weeks ago by
Chris Miller ♦ 20k
0
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Answer:
A: Calling CNVs from WGS data
... It depends on the resolution that you need, but I've called CNVs (fairly large scale) from 1x coverage or less. If you need exact breakpoints, you'll probably need substantially more. ...
written 9 weeks ago by
Chris Miller ♦ 20k
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... My general advice would be to stop using breakdancer. A whole host of more faster, more reliable, and more robust algorithms now exists (manta, lumpy, etc, etc) ...
written 9 weeks ago by
Chris Miller ♦ 20k
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Comment:
C: Code Golf - bisulfite conversion
... When I edited the post, I added a small example! ...
written 10 weeks ago by
Chris Miller ♦ 20k
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4
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Comment:
C: Code Golf - bisulfite conversion
... Updated this post with more details and example input/output. Sorry for the confusion! ...
written 10 weeks ago by
Chris Miller ♦ 20k
0
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4
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432
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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 10 weeks ago by
Chris Miller ♦ 20k
27
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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 10 weeks ago by
Chris Miller ♦ 20k
• updated
10 weeks ago by
zx8754 ♦ 6.1k
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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 12 weeks ago by
Chris Miller ♦ 20k
0
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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 4 months ago by
Chris Miller ♦ 20k
Latest awards to Chris Miller
Commentator
19 hours ago,
created a comment with at least 3 up-votes.
For C: All Possible Substitutions In The Human Reference Genome
Scholar
23 days ago,
created an answer that has been accepted.
For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar
23 days ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Scholar
27 days ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Good Answer
5 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Any Experiences/Solutions For Problems With The Last R Update?
Student
6 weeks ago,
asked a question with at least 3 up-votes.
For Long-Term Hosting For Large Annotation Files?
Student
10 weeks ago,
asked a question with at least 3 up-votes.
For Importing A Large Number Of References From Text
Good Question
10 weeks ago,
asked a question that was upvoted at least 5 times.
For Importing A Large Number Of References From Text
Appreciated
10 weeks ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar
3 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Appreciated
3 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
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Efficiently storing methylation data from BS-sequencing
Scholar
7 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: All Possible Substitutions In The Human Reference Genome
Appreciated
9 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For A: Should I Remove The Unmapped Reads From My Bam ?
Oracle
12 months ago,
created more than 1,000 posts (questions + answers + comments).
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