Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller19k
Reputation:
19,420
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
45 minutes ago
Joined:
8 years, 3 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 • 1,049 results • page 2 of 105 • next >
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Comment: C: Recreate reference fasta from bam file
... really nice solution! ...
written 6 weeks ago by Chris Miller19k
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Comment: C: Recreate reference fasta from bam file
... Nope - the directory with the fasta and the indices was nuked. FWIW, I'm pretty sure that I can recreate this fastq by digging up the vector and gene sequences and spending an hour or two doing manual surgery. It just seems like there oughta be a better way! ...
written 6 weeks ago by Chris Miller19k
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Comment: C: Recreate reference fasta from bam file
... That gives each read in fasta format, not the entire contig.I guess that could be assembled in subsequent steps or something.. ...
written 6 weeks ago by Chris Miller19k
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Recreate reference fasta from bam file
... To make a long story short, I have a bam file that is aligned to the human reference plus a specific contig (human gene + viral vector introduced into a mouse). The fasta file that was used for alignment got inadvertently deleted, but I have good coverage across the contig. Is there a straightfo ...
fasta bam reference written 6 weeks ago by Chris Miller19k • updated 6 weeks ago by h.mon15k
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Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... If given samtools input, copy cat will exclude chromosomes from depth normalization that appear to differ substantially from CN2, based on allele frequency information. This information is more coarse than what you'd get from programs like ABSOLUTE or TITAN_CNA, that use allele frequency but is a q ...
written 8 weeks ago by Chris Miller19k
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Comment: C: normalization when calling CNV areas on a genome-wide scale in tumor-germline sa
... I'd encourage you to use an existing package that rolls these normalizations in, rather than trying to reinvent the wheel. As a self-link, copyCat (https://github.com/chrisamiller/copyCat/) does mapability, GC correction, as well as normalizing global read depth. There are other tools that do simil ...
written 8 weeks ago by Chris Miller19k
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Comment: A: separate one column in two column R
... You're going to want to use the` strsplit()` function with a separator of `""`. Lots of examples can be found with a few searches. ...
written 9 weeks ago by Chris Miller19k
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Comment: C: Bam to BigWig loss of data at MACS peaks (nothing in the BigWig why?)
... Can you edit the question to describe what commands you used to generate the bigwig from the bam? ...
written 10 weeks ago by Chris Miller19k
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Comment: C: Difference Between Somatic And Germline Variant Calling?
... Either you're going to have 0/2 copies, 1/2 copies, or 2/2 copies of that allele. ...
written 11 weeks ago by Chris Miller19k
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Answer: A: How can you sort variants based on their positions from upstream to downstream?
... You really need to provide more information on what kind of file format you have, but for shits and giggles, let's assume it's a bed file with the first three columns: chromsome, start, stop. Sorting is then as easy as: sort -k 1,1 -k 2,2n myfile >outfile ...
written 3 months ago by Chris Miller19k

Latest awards to Chris Miller

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 8 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Oracle 6 months ago, created more than 1,000 posts (questions + answers + comments).
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Should I Remove The Unmapped Reads From My Bam ?
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
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 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Appreciated 7 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
Scholar 8 months ago, created an answer that has been accepted. For A: Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired E
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?

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