Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
Reputation:
20,780
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
9 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 • 1,101 results • page 1 of 111 • next >
1
vote
1
answer
92
views
1
answer
Is read trimming needed for WGBS (bisulfite) data?
... These days read trimming is generally unnecessary in both DNA and RNAseq. Is there any reason why the same shouldn't be true of bisulfite-treated WGBS data? FWIW, we're typically using biscuit for alignments (https://github.com/zwdzwd/biscuit), which is based on bwa-mem. ...
bisufite trimming alignment wgbs written 26 days ago by Chris Miller21k • updated 20 days ago by Devon Ryan93k
0
votes
2
answers
183
views
2
answers
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 3 months ago by Chris Miller21k
2
votes
1
answer
198
views
1
answers
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 4 months ago by Chris Miller21k
3
votes
1
answer
146
views
1
answers
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 4 months ago by Chris Miller21k
1
vote
5
answers
26k
views
5
answers
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 4 months ago by Chris Miller21k
4
votes
3
answers
5.9k
views
3
answers
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 5 months ago by Chris Miller21k
0
votes
0
answers
747
views
0
answers
Job: Bioinformatics Programmer - Washington University in St. Louis
... We currently have an opening for a Bioinformatics Programmer 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 website at ...
analyst developer job genomics cancer written 5 months ago by Chris Miller21k
3
votes
1
answer
384
views
1
answers
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 7 months ago by Chris Miller21k
0
votes
3
answers
1.7k
views
3
answers
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 7 months ago by Chris Miller21k
0
votes
3
answers
400
views
3
answers
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 7 months ago by Chris Miller21k

Latest awards to Chris Miller

Appreciated 16 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Tool To Generate Proportional Venn Diagrams?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 3 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
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
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 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Great Question 6 months ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 6 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 Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 9 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Epic Question 9 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 12 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1242 users visited in the last hour