Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
20,040
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
8 years, 9 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

<prev • 1,073 results • page 1 of 108 • next >
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Comment: C: Finding SNV showing allele specific bias
... You're going to have better luck getting useful answers if you a) show evidence that you've tried to research this problem yourself b) tell us what you've tried, and c) provide more details ...
written 23 hours ago by Chris Miller20k
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Answer: A: Get Flanking Amino Acid Sequence
... Highly suggest that you check out the [pVACtools](https://pvactools.readthedocs.io/en/latest/) suite, which utilizes some VEP plugins and custom parsing to extract exactly this information and format it nicely prior to doing binding affinity predictions. ...
written 10 days ago by Chris Miller20k
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Answer: A: Getting same SNPs both in cancer and normal files when seen in IGV - Integrativ
... > To get SNPs specific to horn cancer, I have subtract Horn Normal vcf file from Horn Cancer vcf file using bedtools. Don't do this. The assumptions that germline variant callers make about VAF distributions and such don't lend themselves well to calling cancer variants. You need to use a true s ...
written 10 days ago by Chris Miller20k
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Comment: C: a question about fishplot
... I should mention that you can also dig into the drawing code if you really want to tweak things. If you come up with useful options, pull requests are welcome! ...
written 28 days ago by Chris Miller20k
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Answer: A: a question about fishplot
... That has to do with the way that the splining function is generating curves to fit your points. Unfortunately, the goals of having perfectly smooth curves and conforming precisely to the values you enter are mutually exclusive (or at least quite difficult!) If you want a perfectly smooth one, you ca ...
written 28 days ago by Chris Miller20k
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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 weeks 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 9 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 9 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 9 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 9 weeks ago by Chris Miller20k

Latest awards to Chris Miller

Commentator 23 hours ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 23 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 27 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 6 weeks ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 10 weeks ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 10 weeks ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 10 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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
Scholar 4 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 7 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 9 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 12 months ago, created more than 1,000 posts (questions + answers + comments).

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