Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
11 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.

Posts by Chris Miller

<prev • 1,035 results • page 1 of 104 • next >
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Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... If given samtools input, copy cat will exclude chromosomes from depth normalization that appear to differ substantially from CN2, based on allele frequency information. This information is more coarse than what you'd get from programs like ABSOLUTE or TITAN_CNA, that use allele frequency but is a q ...
written 11 hours ago by Chris Miller19k
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Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... I'd encourage you to use an existing package that rolls these normalizations in, rather than trying to reinvent the wheel. As a self-link, copyCat (https://github.com/chrisamiller/copyCat/) does mapability, GC correction, as well as normalizing global read depth. There are other tools that do simil ...
written 1 day ago by Chris Miller19k
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Comment: A: separate one column in two column R
... You're going to want to use the` strsplit()` function with a separator of `""`. Lots of examples can be found with a few searches. ...
written 3 days ago by Chris Miller19k
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Comment: C: Bam to BigWig loss of data at MACS peaks (nothing in the BigWig why?)
... Can you edit the question to describe what commands you used to generate the bigwig from the bam? ...
written 15 days ago by Chris Miller19k
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Comment: C: Difference Between Somatic And Germline Variant Calling?
... Either you're going to have 0/2 copies, 1/2 copies, or 2/2 copies of that allele. ...
written 21 days ago by Chris Miller19k
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Answer: A: How can you sort variants based on their positions from upstream to downstream?
... You really need to provide more information on what kind of file format you have, but for shits and giggles, let's assume it's a bed file with the first three columns: chromsome, start, stop. Sorting is then as easy as: sort -k 1,1 -k 2,2n myfile >outfile ...
written 5 weeks ago by Chris Miller19k
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Answer: A: IGV - is there a way to extract bulk information?
... My script here has some useful code if you're going to be submitting this to a cluster/running headless: https://github.com/chrisamiller/igvScreenshot ...
written 6 weeks ago by Chris Miller19k
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Answer: A: samtools view: failed to open "sort" for reading: No such file or directory
... Why not just this? bwa mem -t2 -R '@RG\tID:NA12878\tSM:NA12878\tLB:NA12878' genome.fa SRR1611183_1.fastq.gz SRR1611183_2.fastq.gz | samtools sort -@2 - > SRR1611183.bam ...
written 6 weeks ago by Chris Miller19k • updated 6 weeks ago by Ram14k
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Comment: C: WGS coverage (depth) for CNV detection
... 1) Look at Figure 2a in that paper. 2) There isn't a simple conversion factor of that type. You're going to be taking data that is somewhat noisy, testing different bin sizes, then (possibly) running it through correction for gc-bias/mapability, then (definitely) using a segmentation algorithm t ...
written 7 weeks ago by Chris Miller19k
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Answer: A: WGS coverage (depth) for CNV detection
... It's not quite that straightforward, but you have the right general idea. My old paper on the readDepth package has some simulations that explicitly address this question: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016327 ...
written 7 weeks ago by Chris Miller19k

Latest awards to Chris Miller

Commentator 3 days ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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?
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
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
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: 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?
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Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 6 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
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why Should I Use Galaxy ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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: 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?

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