Moderator: Obi Griffith

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Obi Griffith17k
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Washington University, St Louis, USA
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obigriffith
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I am an Assistant Professor of Medicine (Oncology) and Genetics at Washington University School of Medicine and Assistant Director at the McDonnell Genome Institute. I study cancer genomics, primarily through clinical statistics and bioinformatic analyses of next-generation sequence data such as whole genome (WGS), exome, and transcriptome (RNA-seq) data.

Posts by Obi Griffith

<prev • 420 results • page 2 of 42 • next >
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Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... Thanks for the comments! 1. I don't think this has to do with a general Alu repeat low complexity, low mapping quality issue. The reads in these peaks and both reads of the discordant pairs almost entirely have normal (very good) mapping qualities. In any case, if it just had to do with mapping is ...
written 22 months ago by Obi Griffith17k
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Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS data
... OK. I realize this is not exactly a bioinformatics question but I know that a lot of people in this forum spend their days staring at NGS alignments and am hoping someone has an explanation or some insight. See the IGV screenshot below of representative matched tumor and normal samples. The pattern ...
wgs ngs alignment sequencing written 22 months ago by Obi Griffith17k • updated 22 months ago by WouterDeCoster35k
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Comment: C: Plotting numbers of somatic substitutions per megabase (MB)
... Are you supplying the Alexandrov example just to demonstrate layout? I ask because this figure has a lot more going on than just mutations/MB. It is showing mutations/MB brokend down by mutation type in several different ways. If that is what you want then it is a complicated question/answer. ...
written 23 months ago by Obi Griffith17k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... Yes. Just look at the format of the "mutation_data" object. If you can add another column with VAF values then you should be able to just specify mainLabelCol="X" where X is the name of your new VAF column rather instead of "amino.acid.change". ...
written 24 months ago by Obi Griffith17k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... I'm not sure what you are asking. Do you mean the variant allele frequency for each gene/sample? As a text value in each cell? Or, something else? ...
written 24 months ago by Obi Griffith17k
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Comment: C: Announcing new Bioinformatics Workshops in NYC: Apr 27 - May 3, 2015
... Hello Obi Griffith! We believe that this post does not fit the main topic of this site. Old workshop now outdated. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a repl ...
written 2.0 years ago by Obi Griffith17k
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Comment: C: How to create a mutation lolliplot with GenVisR
... Perhaps @zlskidmore could comment. ...
written 2.3 years ago by Obi Griffith17k
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Answer: A: TCR Sequencing Lack of Repertoire Overlap
... Another formal possibility is that your mice are not as isogenic as you think. I have had several experiences where we were operating on the assumption that highly inbred lab mouse strains are "genetically identical" but in fact upon whole genome sequencing determine that substantial genetic diversi ...
written 2.5 years ago by Obi Griffith17k
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Comment: C: Cost Comparison Between Microarray And Rna-Seq Experiment
... This answer is now quite out of date with respect to RNAseq costs. These still vary widely depending on the protocol, target number of reads, etc. However to update the ballpark numbers I estimate that a typical RNA experiment starting from isolated RNA (including sample management, Illumina TruSeq ...
written 2.5 years ago by Obi Griffith17k
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... You can set dendrogram="none" to stop drawing the dendrograms. To stop actual clustering you can set Rowv=FALSE and/or Colv=FALSE depending on which dimension(s) you don't want clustering for. If you turn off both, you could also drop the hclustfun and distfun parameters since these will have no use ...
written 2.5 years ago by Obi Griffith17k

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