Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
Reputation:
20,750
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
9 years, 7 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 • 1,100 results • page 1 of 110 • next >
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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 7 weeks 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 3 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 3 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 3 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 3 months ago by Chris Miller21k
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Job: Bioinformatics Developer/Analyst - Washington University in St. Louis
... We currently have an opening for a Bioinformatics Developer/Analyst in our cancer genomics group at Washington University in St. Louis. It's a great place to work, a fantastic place to do science, and a great opportunity for a talented coder to learn bioinformatics. Apply through the WUSTL jobs web ...
analyst developer job genomics cancer written 3 months ago by Chris Miller21k
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Answer: A: Free for academic use only licenses (If you want to sell your software please ju
... Appreciate the perspective! I've navigated this from the academic side before, and it's tough. We all know that academic software has a reputation for being poorly engineered, and unsupported approximately 5 minutes after it's published. That's because it's _really_ hard to get grant funding for st ...
written 5 months ago by Chris Miller21k
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Comment: C: Bin chromosome every 1kb and get average value
... Even though Pierre has created a strange little masterpiece up there, I think this is going to be the best answer for most people :) ...
written 5 months ago by Chris Miller21k
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Comment: C: HGVS format to VCF from portal.gdc.cancer.gov
... If this works for you, great, but IIRC, that's not valid VCF format, because of the missing "anchor bases" for ins and del. (e.g. G/- should be CG/C) A lot of tools will get angry about that. VEP will fill those in with the missing ref bases, if you do end up needing them. ...
written 6 months ago by Chris Miller21k
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Answer: A: HGVS format to VCF from portal.gdc.cancer.gov
... Those are essentially genomic coordinates, right? I think you could just parse out the extra crap then give it to VEP to create a valid VCF: https://m.ensembl.org/info/docs/tools/vep/vep_formats.html#default I've done similar things to get wacky formats into VCF ...
written 6 months ago by Chris Miller21k

Latest awards to Chris Miller

Good Answer 24 days ago, created an answer that was upvoted at least 5 times. For A: Tool To Generate Proportional Venn Diagrams?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 12 weeks 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
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
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
Great Question 4 months ago, created a question with more than 5,000 views. For Biomart Very Slow
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 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
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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 8 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Epic Question 8 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 10 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 10 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 11 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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