Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
Reputation:
17,690
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Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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Google Scholar Page
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an hour ago
Joined:
7 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 • 938 results • page 1 of 94 • next >
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Answer: A: Generate column names on the fly R
... You'll probably want to look into the `scan()` function, and use the `nlines` parameter. https://stat.ethz.ch/R-manual/R-devel/library/base/html/scan.html Off the top of my head, I might do something like: 1) read in the first 100 lines of the file with scan, keep only those that match my comment ...
written 1 day ago by Chris Miller18k
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Comment: C: StackExchange/Area51 bioinformatics is back
... It's fair, and I don't expect Istvan to single-handedly shoulder the load. It would be great to have a development roadmap that's transparent to the community, as well as recruitment of contributors (paid or volunteer), if the platform is going to continue to grow. Right now, things seem to have st ...
written 2 days ago by Chris Miller18k
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Comment: C: StackExchange/Area51 bioinformatics is back
... This is a good point - Tutorials and the Job Board, in particular are really nice. ...
written 2 days ago by Chris Miller18k
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Answer: A: StackExchange/Area51 bioinformatics is back
... I can see why lousy search, difficult UI, etc are frustrating to some folks. BioStars has the community and knowledgebase, but there doesn't seem to be a clear plan to improve the site, and reach feature parity with SE. Istvan, would you care to weigh in on those topics? More than anything, I just ...
written 2 days ago by Chris Miller18k
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Answer: A: bam-readcount values are higher than Mutect results
... Many callers do some filtering of reads first (by base quality, by mapping quality, maybe even local realignment) and report only counts from reads that pass. bam-readcount, by default, outputs "raw" counts. You may or may not be able to mimic those Mutect settings with bam-readcount parameters. ...
written 3 days ago by Chris Miller18k
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Comment: C: Bam-readcount output empty from certain regions (RNA seq bams)
... The details are fuzzy in my mind at the moment, but I suspect there is a difference between sites with coverage, where all reads fail quality checks (0) vs sites without any coverage (not output). ...
written 4 days ago by Chris Miller18k
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Answer: A: Bam-readcount output empty from certain regions (RNA seq bams)
... Yes, if there is no coverage of your variant, then bam-readcount will return nothing for that site. This includes sites for which there are no reads that meet your filtering criteria. ...
written 5 days ago by Chris Miller18k
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Answer: A: bam-readcount tool: output zero coverage bases
... You are correct that bam-readcount does not output zero-coverage bases. It requires a little post-processing to add those back in. (such as what's done here https://github.com/genome/genome/blob/master/lib/perl/Genome/Model/Tools/Analysis/Coverage/BamReadcount.pm) ...
written 5 days ago by Chris Miller18k
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Answer: A: How to plot mutation hotspot according to mutation counts
... There are several R packages and online tools, but I'd probably start with http://www.cbioportal.org/mutation_mapper.jsp ...
written 5 days ago by Chris Miller18k
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Comment: C: What is Copy Number Variation(CNV) and Alteration(CNA)
... One more comment - the example you give, of `GCGATGA` appearing more than once, is usually referred to as an indel. Generally speaking, SV/CNVs are bigger than 1kb, indels are smaller than 100bp, and there's also a weird middle range where the terms are often mixed. ...
written 22 days ago by Chris Miller18k

Latest awards to Chris Miller

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 2 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 19 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 12 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
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: Extract Base Based On Position From Bam File
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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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?
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 8 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"

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