Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
Reputation:
21,080
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Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
3 days, 15 hours ago
Joined:
10 years, 4 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.

Posts by Chris Miller

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Effects of applying BQSR twice?
... Does anyone have insight into what happens if you apply BQSR twice to a sample? The case here is that we might run a pipeline that aligns and runs BQSR, then we throw away the original fastqs. If we later want to realign, we can regenerate fastqs, but the original quality scores are gone. What wou ...
qualityscores bqsr alignment sequencing written 3 days ago by Chris Miller21k • updated 3 days ago by h.mon30k
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Comment: C: How to distinguish subclone from sciClone or PyClone result
... Usually that is the case ...
written 9 weeks ago by Chris Miller21k
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Answer: A: How to distinguish subclone from sciClone or PyClone result
... The founding clone is made up of the set of mutations that is in every cell of the tumor. It generally corresponds to the highest-VAF clone (which should be highest in all samples) ...
written 10 weeks ago by Chris Miller21k
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Answer: A: Sciclone cluster all around y=x
... This may in fact be the case - some tumors do not evolve much over time, or are largely homogeneous, in which case you would expect to see everything on the diagonal! ...
written 10 weeks ago by Chris Miller21k
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Is read trimming needed for WGBS (bisulfite) data?
... These days read trimming is generally unnecessary in both DNA and RNAseq. Is there any reason why the same shouldn't be true of bisulfite-treated WGBS data? FWIW, we're typically using biscuit for alignments (https://github.com/zwdzwd/biscuit), which is based on bwa-mem. ...
bisufite trimming alignment wgbs written 7 months ago by Chris Miller21k • updated 7 months ago by Devon Ryan95k
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Answer: A: Removing white space from the beginning of the second field (sequence) in a fast
... if this is a fasta file, then you'll always want to remove leading whitespace, so something like: sed 's/^\s//' myfile.fa oughta work fine ...
written 10 months ago by Chris Miller21k
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Answer: A: Using Varscan without a matched normal
... Somatic calling is essentially just calling differences between two samples. If you use a tumor as your control and a metastasis as your case, then you'll call metastasis-specific mutations (but will miss any somatic mutations shared between the tumor and met). ...
written 11 months ago by Chris Miller21k
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Answer: A: How can I get this sorted by ascending order? (when the number and character is
... If you're using GNU sort, then "sort -V" will do what you want. In general, though, it's not necesary. The community has (somewhat) standardized on character sort order, which is what you have there. ...
written 11 months ago by Chris Miller21k
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Comment: C: How Can I Know The Length Of Mapped Reads From Bam File?
... Sure - make it `samtools view -F 4 file.bam ...` if you want only mapped ...
written 11 months ago by Chris Miller21k
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Answer: A: Tool to separate human and mouse rna seq reads
... We're testing out [XenoSplit](https://github.com/goknurginer/XenoSplit) right now and it seems to work fairly well. I've also used [NGS-disambiguate](https://github.com/AstraZeneca-NGS/disambiguate) in the past with success. ...
written 12 months ago by Chris Miller21k

Latest awards to Chris Miller

Commentator 4 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Popular Question 5 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 months ago, created an answer that has been accepted. For A: Modifying A Gene Sequence With Personal Snps?
Scholar 6 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar 6 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Tool To Generate Proportional Venn Diagrams?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 11 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 11 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Great Question 13 months ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 13 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

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