Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
19,890
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
37 minutes ago
Joined:
8 years, 8 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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Answer: A: How to load BAM files that do not have chromosome name in the header?
... It looks like you have a sequence data that was aligned to a transcriptome, rather than a genome. If you want to use IGV, you will either need to a) create a new "genome" for IGV with one contig per gene (this is almost certainly not what you want) or b) align your RNAseq data to a genome, using s ...
written 4 days ago by Chris Miller20k
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Some tumors have it, some don't. To the best of my knowledge, the GDC (https://portal.gdc.cancer.gov/) is currently the canonical source for TCGA data. ...
written 5 weeks ago by Chris Miller20k
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Answer: A: How can I find motifs under individual ATAC-peaks?
... This tool accepts a peak file, and looks for enriched motifs under those peaks: http://homer.ucsd.edu/homer/ngs/peakMotifs.html ...
written 5 weeks ago by Chris Miller20k
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Answer: A: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Those are somatic mutations and are all called in the tumor samples relative to the normal. Germline mutations are protected with an additional level of restrictions, but are available, but almost certainly in VCF, not MAF format. ...
written 5 weeks ago by Chris Miller20k
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Comment: C: Google announces DeepVariant
... While essentially saying that germline calling is a solved problem is probably a little bit of a stretch, it's absolutely not true for somatic calling. Tumor ploidy and purity come into play, FFPE may be involved, or you might be looking for very low-frequency events, etc. There's a lot of complexit ...
written 5 weeks ago by Chris Miller20k
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Comment: C: Google announces DeepVariant
... Mark isn't trying to hide that fact - consider your post the disclaimer! ...
written 5 weeks ago by Chris Miller20k
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Comment: C: SciClone on WES data
... You can also just add the `cnCallsAreLog2=TRUE` param when running sciclone ...
written 5 weeks ago by Chris Miller20k
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Answer: A: Calling CNVs from WGS data
... It depends on the resolution that you need, but I've called CNVs (fairly large scale) from 1x coverage or less. If you need exact breakpoints, you'll probably need substantially more. ...
written 5 weeks ago by Chris Miller20k
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Comment: C: bam2cfg.pl not able to find statistics : Breakdancer
... My general advice would be to stop using breakdancer. A whole host of more faster, more reliable, and more robust algorithms now exists (manta, lumpy, etc, etc) ...
written 5 weeks ago by Chris Miller20k
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Comment: C: Code Golf - bisulfite conversion
... When I edited the post, I added a small example! ...
written 5 weeks ago by Chris Miller20k

Latest awards to Chris Miller

Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 16 days ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 5 weeks ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 5 weeks ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 9 weeks 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
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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 6 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 8 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 11 months ago, created more than 1,000 posts (questions + answers + comments).
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Appreciated 11 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
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

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