Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
Reputation:
18,600
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
20 hours ago
Joined:
7 years, 8 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.

Posts by Chris Miller

<prev • 991 results • page 2 of 100 • next >
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Answer: A: Mapping mutations to TCGA samples
... I did a lot of the analysis for the TCGA AML paper. The simplest way to pull mutations is to go to the [paper's supplemental site](https://tcga-data.nci.nih.gov/docs/publications/aml_2012/) and pull Supplemental Table 6. Note that the variants are all on build 36, so liftover may be in order if you ...
written 16 days ago by Chris Miller19k
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Answer: A: perplexity value in t-sne algorithm
... Though not super in-depth, this post is a good primer: [How to Use t-SNE Effectively ](https://distill.pub/2016/misread-tsne/) ...
written 22 days ago by Chris Miller19k
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Answer: A: how to read indexed bamfiles
... > samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai You should point samtools to the bam file, not the index file. ...
written 28 days ago by Chris Miller19k
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Comment: C: WGS data for healthy human women sequenced on Illumina HiSeq 2000?
... Large chunks of the TCGA cohorts would have been sequenced on the 2000, and I think that information will be obtainable, buried deep in the metadata somewhere. ...
written 6 weeks ago by Chris Miller19k
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Comment: C: pindel not picking up on a lab-made gene knockout deletion
... What's are the sizes of the deletion and insertion? Large events, especially, are hard to detect with pindel (and many other tools), because read mapping is often poor. ...
written 6 weeks ago by Chris Miller19k
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Answer: A: SciClone Cluster Number
... Yes, the 0 cluster contains outlier points that were excluded from analysis. ...
written 6 weeks ago by Chris Miller19k
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Comment: C: Concept of Matched normal vs. Virtual Normal
... 1) The only real concern is that the normal should be as free from tumor contamination as possible. Blood is a fine control for most solid tumors, but leukemias are trickier, as you often find tumor contamination in the skin. I think I remember that skin samples from lymphoma patients tend to be fr ...
written 7 weeks ago by Chris Miller19k
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Comment: C: CNV detection from RNA-seq data
... Yeah, I saw Aviv talk at a conference, but that seems like the right paper. Even more flabbergasted that it works with single-cell RNAseq. Amazing stuff! ...
written 7 weeks ago by Chris Miller19k
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Comment: C: sciClone input LOH
... Yep, that's the definition you're looking for. Hope it cleared things up! ...
written 7 weeks ago by Chris Miller19k
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Answer: A: Does Genome MuSiC use soft-clipped bases in its coverage calculation?
... I believe that the answer is no, as it's using the samtools libraries, and those do not return soft-clipped bases by default, IIRC. That said, it'd be easy to verify. Extract a dozen reads from a region of your bam file, choose a position that has both soft-clipped and non-soft-clipped bases, then r ...
written 7 weeks ago by Chris Miller19k

Latest awards to Chris Miller

Scholar 9 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Appreciated 15 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 16 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 28 days 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
Scholar 28 days ago, created an answer that has been accepted. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Why Should I Use Galaxy ?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Popular Question 3 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Popular Question 3 months ago, created a question with more than 1,000 views. For Will Picard MarkDuplicates also un-mark duplicates?
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Epic Question 5 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 5 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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