Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
Reputation:
18,080
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
2 days, 6 hours ago
Joined:
7 years, 5 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 • 961 results • page 1 of 97 • next >
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Answer: A: sciClone: Multiple alleles at single position
... SciClone doesn't actually care what the position is, and it'd be a nice fix to change the code to reflect that (pull requests welcome). As a quick fix, though, I'd recommend just changing the sciclone inputs to something unique. if your variants look like: 1 123456 A/T 1 123456 A/C Th ...
written 10 days ago by Chris Miller18k
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Answer: A: Low reads mapping in methylation sequencing
... Pull them up in IGV - did you get read-through into the adapters? Then adapter trimming might help. You might also try using a methylation aware aligner (BSmap, Biscuit, etc)/ ...
written 4 weeks ago by Chris Miller18k
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Comment: C: Bioinformatics position at Washington University
... I'll vouch for this lab and some of the cool science they're doing! ...
written 6 weeks ago by Chris Miller18k
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Comment: C: The meaning of VAF and LOH in sciclone
... There may sometimes be non-reference, non-primary-variant reads - for example: 1 12345 A T Counts: A: 99 C: 2 G: 0 T: 99 VAF: 49.5% ...
written 6 weeks ago by Chris Miller18k
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Answer: A: "TRUE" instead of "T" allele in R
... I suspect that using "read.table( . . . stringAsFactors=F)" will solve your problem. (edit - it will not! see the comprehensive answer above) ...
written 9 weeks ago by Chris Miller18k
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Answer: A: TCGA clinical data, info about treatment_id / drug
... None of the TCGA tumors were treated prior to sequencing: > Neoadjuvant treatment was not allowable TCGA's goal was to accelerate > the understanding of the underlying genomics of primary, untreated > tumors. Cancer treatment can involve mutagens or carcinogens which > could cloud the o ...
written 9 weeks ago by Chris Miller18k
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Comment: C: I have a problem when I am using the bedGraphToBigWig.
... It sounds like one of your input files is not what you expect (and that you accidentally downloaded an html file instead of a bed file) ...
written 9 weeks ago by Chris Miller18k
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Answer: A: Error when running Genome MuSiC: no smg genes
... I don't know your exact issue, but this seems to be the key line in the output: Skipped 1054 mutation(s) that belong to unrecognized samples Check that your sample names all match up as expected. ...
written 9 weeks ago by Chris Miller18k
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Comment: C: SciClone Viewport 'panel.3-4-3-4' was not found
... Hello lancet_junyu! As is, this question is unanswerable, so I'm closing it. As I told you over email, please try again, providing a detailed summary of the code you were trying to run, the output of sessionInfo(), and the output of traceback(), run just after the error occurs. Thanks ...
written 9 weeks ago by Chris Miller18k
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Answer: A: Can Bedtools be used to find features that exist in one bed file, but not in two
... bedtools intersect -a FILE1 -b <(cat FILE2 FILE3 | bedtools sort) -v >OUTFILE ...
written 9 weeks ago by Chris Miller18k

Latest awards to Chris Miller

Popular Question 5 days ago, created a question with more than 1,000 views. For Will Picard MarkDuplicates also un-mark duplicates?
Popular Question 5 days ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Appreciated 6 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Epic Question 8 weeks ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 10 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
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Popular Question 5 months ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
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Appreciated 6 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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