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Chris Miller

Chris Miller

Bioinformatics Grad student at Baylor College of Medicine. My online home is at
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As of 6:09 am today, I am over 1 billion seconds old. Here's to another two billion at least!
Oligotyping analysis of the human oral microbiome and solid commentary by Carl Zimmer
Just saw "In the late 1900s" used to describe when DNAseq was starting. Seems awfully historical for something that's just really taking off
Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease
RT @tomtomorrow: It's almost as if the linkage between employment and health care is a fundamentally terrible idea.
Maybe this will lead to the government just giving out birth control. Would be a nice first step towards single payer healthcare. #SCOTUS
"It is a good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast" - Konrad Lorenz
RT @michelledean: A startling bit, in which Alito basically says, “no worries, this applies only to women’s health”
RT @ACLU: Never before has #SCOTUS said employers can use their religious beliefs to deny employees a benefit they are guaranteed by law to receive.
RT @BorowitzReport: I worry that the US embracing soccer will lead to other things Europe does, like recognizing climate change and offering maternity leave.
RT @random_walker: Google Scholar should rename the "Recommended based on My Citations" page to "Papers that should cite my work but don't."
Want to live in a walkable area in STL? These are your options (and some are a stretch). Via
RT @matthewbaldwin: An easy way to get pizza sauce off the ceiling is to not have children. #lifehack
RT @GlennF: Maybe if a Republican senator found out one of his children was climate change.
bc it makes too much sense: "Why not share the cost of paying for roads in proportion to the usage made of roadways?"
Answer: A: Identifying the tumor clones and subclones with VAF from VarScan2 -
We built the sciClone package for exactly this purpose: It takes inputs of somatic mutations, with readcounts and VAFs, and uses that information to infer subclonal populations in heterogeneous tumors. It also gives you some nice visualization options. - Chris Miller
Comment: C: Will Picard MarkDuplicates also un-mark duplicates? -
Well played, sir.  In retrospect, doing the experiment myself would have been faster than that 10 minutes of searching and typing this post.  Thanks! - Chris Miller
Will Picard MarkDuplicates also un-mark duplicates? -
If I take a bam that's already aligned and has dups marked, remove a bunch of reads, then re-run Picard's mark-duplicates, will it correctly change the flags of reads that are no longer duplicates (but may have been before ditching the reads)? This question is proving surprisingly hard to google for. - Chris Miller
Vaccination works. Measles Incidence Rate Per 100,000 People, 1928 - 2003 (via
For all the policymakers that still don't get it: Building Bigger Roads Actually Makes Traffic Worse.
Comment: C: How to make this kind of 3-D plotting for cancer subclones ? (picture attached) -
- Are your VAFs scaled between 0 and 100 (percentage) and not between 0 and 1 (fraction)? - If your data really does look like this, you could modify with the sc.plot2d function in the R code to tweak the xlim and ylim. - Chris Miller
Comment: C: Applying a task to several files in R -
I'm closing this up, since it's not a bioinformatics question, as noted below. This allow us to keep the site focused on the topics that the community can help with.  Please consider asking your question on Stack Overflow, or better yet, taking a little time to work through a basic R tutorial, which will help with both of the questions you've asked today. - Chris Miller
Comment: C: Would You Be Interested In Having A Usesthis Like Site For The Bioinformatics Co -
Sure, but you're going to have to give me a little time to get my thoughts together. If you haven't heard from me in a week or so, shoot me an email and remind me - Chris Miller
Answer: A: Software To Call Somatic Indels? -
Pindel is another generally good somatic indel caller: - Chris Miller
Comment: C: How Can I Create A Protein-Protein Interface Schematic Or Diagram For Easy Viewi -
I don't know which program that is, but if you need to visualize networks/interactions, Cytoscape is often the answer. - Chris Miller
Answer: A: Applying a task to several files in R -
here's some example code > files = Sys.glob("*.txt") > files [1] "1.txt"     "2.txt"     "3.txt" > for(i in files){   #your code here } Now I'm closing this up, since it's really a programming question and not a bioinformatics question.  Based on your last two questions, you would benefit from working through a short R tutorial. - Chris Miller
Comment: C: How to make this kind of 3-D plotting for cancer subclones ? (picture attached) -
1) That's not your sequencing coverage, that's the VAF. Seeing the highest clone at sub-20% suggests that your tumor purity is very low.  2) Those outlier points (and corresponding strange clusters) would almost certainly be cleaned up by adding copy-number information. You can derive it from exome data using VarScan, cn.mops, or other packages. - Chris Miller
Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics? -
You also occasionally see IUPAC codes pop up in fasta sequences. - Chris Miller
Comment: C: How Can I Create A Protein-Protein Interface Schematic Or Diagram For Easy Viewi -
Nice detective work! That link didn't work for me, so I pointed it to the pubmed page - Chris Miller
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