Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller18k
Reputation:
18,020
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
1 day ago
Joined:
7 years, 4 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 • 960 results • page 1 of 96 • next >
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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 9 days 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 21 days 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 22 days 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 5 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 5 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 5 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 6 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 6 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 6 weeks ago by Chris Miller18k
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Answer: A: overlap BED files, but account for region name
... Your proposal of splitting into separate files by name seems reasonable to me. If that's not satisfying, nothing is stopping you from writing a 20-line perl script that does the intersection in a name-aware manner. Genome set operations aren't hard, it's just more convenient to use existing tools. ...
written 6 weeks ago by Chris Miller18k

Latest awards to Chris Miller

Appreciated 20 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Epic Question 5 weeks ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Scholar 6 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 6 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Exon Array Analysis Tools
Scholar 12 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 12 weeks 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 3 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 3 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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 4 months ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
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?

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