RT @GraveleyLab: Please don't put the impact factor of the journal your papers are in on your CV!
Jul 23, 2014
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Chris Miller
Bioinformatics Grad student at Baylor College of Medicine. My online home is at http://www.chrisamiller.com/
RT @kerencarss: This is an important article. WGS has better coverage uniformity than WES, and less bias in variant calling. http://www.biomedcentral.com/1471-21...
Jul 21, 2014
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You’re not allowed bioinformatics anymore http://biomickwatson.wordpress.com/2014...
Jul 21, 2014
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Answer: A: Puzzle on size of Bam file - https://www.biostars.org/p...
Jul 19, 2014
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Like Istvan said - don't worry about the size, count the number of lines in your bam file to see the effect.
- Chris Miller
Answer: A: sciClone error with analysis - https://www.biostars.org/p...
Jul 17, 2014
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Make sure the results/ folder exists before running the script. I'll check the code in the morning and push a change if need be.
- Chris Miller
Comment: C: Identifying the tumor clones and subclones with VAF from VarScan2 - https://www.biostars.org/p...
Jul 16, 2014
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Sorry for the slow response, I've been out of town.
Short answer: That input is optional and may not be relevant to all cancers, so you may be fine without it.
Long answer: I believe we take the frequencies of germline SNPs in the tumor genome and look for large regions where there are no het sites, caused by CN-neutral LOH (aka UPD). You can segment them into discrete regions using CBS, as implemented in the DNAcopy package for R. Plotting on a per-chromosome basis should also make them clearly evident, if they exist.
- Chris Miller
“Remember kids, the only difference between screwing around and science is writing it down.” --Adam Savage
Jul 15, 2014
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RT @sween: ☆。★。☆。★ 。☆ 。☆。☆ ★。＼｜／。★ oh my god stop complaining ★。／｜＼。★ 。☆。。☆ ☆。★。 ☆ ★
Jul 15, 2014
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RT @fakethirtyeight: We surveyed 10,752 people about data visualization. The results: https://twitter.com/fakethi...
Jul 14, 2014
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RT @PlantEvolution: Several #MPMI2014 speakers talking of “our bioinformatician” w/o mentioning names - bioinformaticians aren’t pets! #bioinformatics
Jul 13, 2014
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New Challenges of Next-Gen Sequencing http://massgenomics.org/2014...
Jul 10, 2014
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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!
Jul 9, 2014
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Oligotyping analysis of the human oral microbiome http://www.pnas.org/content... and solid commentary by Carl Zimmer http://phenomena.nationalgeographic.com/2014...
Jul 6, 2014
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Just saw "In the late 1900s" used to describe when DNAseq was starting. Seems awfully historical for something that's just really taking off
Jul 6, 2014
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Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease http://www.biomedcentral.com/1471-21...
Jul 6, 2014
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RT @tomtomorrow: It's almost as if the linkage between employment and health care is a fundamentally terrible idea.
Jun 30, 2014
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Maybe this will lead to the government just giving out birth control. Would be a nice first step towards single payer healthcare. #SCOTUS
Jun 30, 2014
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"It is a good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast" - Konrad Lorenz
Jun 30, 2014
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RT @michelledean: A startling bit, in which Alito basically says, “no worries, this applies only to women’s health” https://twitter.com/michell...
Jun 30, 2014
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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.
Jun 30, 2014
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RT @BorowitzReport: I worry that the US embracing soccer will lead to other things Europe does, like recognizing climate change and offering maternity leave.
Jun 29, 2014
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RT @random_walker: Google Scholar should rename the "Recommended based on My Citations" page to "Papers that should cite my work but don't."
Jun 27, 2014
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Want to live in a walkable area in STL? These are your options (and some are a stretch). Via http://m.stltoday.com/news... https://twitter.com/chrisam...
Jun 22, 2014
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RT @matthewbaldwin: An easy way to get pizza sauce off the ceiling is to not have children. #lifehack
Jun 22, 2014
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RT @GlennF: Maybe if a Republican senator found out one of his children was climate change.
Jun 21, 2014
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bc it makes too much sense: "Why not share the cost of paying for roads in proportion to the usage made of roadways?" http://news.stlpublicradio.org/post...
Jun 20, 2014
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Answer: A: Identifying the tumor clones and subclones with VAF from VarScan2 - https://www.biostars.org/p...
Jun 19, 2014
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We built the sciClone package for exactly this purpose: https://github.com/genome...
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? - https://www.biostars.org/p...
Jun 19, 2014
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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? - https://www.biostars.org/p...
Jun 18, 2014
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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 http://www.reddit.com/r...) https://twitter.com/chrisam...
Jun 18, 2014
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For all the policymakers that still don't get it: Building Bigger Roads Actually Makes Traffic Worse. http://www.wired.com/2014...
Jun 18, 2014
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RT @VoteNoOnSeven: Via the @columbiatribune: Who pays? http://t.co/GhwLLxt67W http://t.co/Wv6OODiRyC
Jun 17, 2014
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