Moderator: Obi Griffith

gravatar for Obi Griffith
Obi Griffith14k
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Washington University, St Louis, USA
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http://www.obigriffith...
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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 • 412 results • page 1 of 42 • next >
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Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... You are indeed correct that GC/AT content correlates with Alu elements. In general Alu elements seem to be correlated with more GC-rich regions, although it depends on the type/age of the Alu element (and is probably [more complicated][1] than that). Indeed the very top track in the IGV snapshot sho ...
written 19 days ago by Obi Griffith14k
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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 19 days ago by Obi Griffith14k
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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 21 days ago by Obi Griffith14k • updated 20 days ago by WouterDeCoster13k
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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 5 weeks ago by Obi Griffith14k
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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 9 weeks ago by Obi Griffith14k
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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 9 weeks ago by Obi Griffith14k
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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 10 weeks ago by Obi Griffith14k
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Comment: C: How to create a mutation lolliplot with GenVisR
... Perhaps @zlskidmore could comment. ...
written 6 months ago by Obi Griffith14k
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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 8 months ago by Obi Griffith14k
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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 8 months ago by Obi Griffith14k

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Student 19 days ago, asked a question with at least 3 up-votes. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 4 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Popular Question 6 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Great Question 6 months ago, created a question with more than 5,000 views. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Great Question 6 months ago, created a question with more than 5,000 views. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Scholar 7 months ago, created an answer that has been accepted. For A: What read lengths are produced by modern Illumina sequencers?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 8 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 8 months ago, created a question with more than 1,000 views. For Consent and privacy issues arising from the sequencing of cell lines
Popular Question 8 months ago, created a question with more than 1,000 views. For Consent and privacy issues arising from the sequencing of cell lines
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Gold Standard 10 months ago, created a post with more than 25 bookmarks. For Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets

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