User: Isaac Joseph

gravatar for Isaac Joseph
Isaac Joseph80
Reputation:
80
Status:
Trusted
Location:
Berkeley, CA USA
Last seen:
1 week ago
Joined:
6 years, 10 months ago
Email:
i********@gmail.com

Working on improving Agilent's target enrichment (e.g. exome sequencing) assays via rational/data-driven machine learning techniques.

Received Ph.D. from U.C. Berkeley in 2016 under Lior Pachter and Joseph F. Costello. Focused on creating new machine-learning classification algorithms for cancer genomic data. 

B.S. in C.S. from MIT in 2011. 

 

 

 

Posts by Isaac Joseph

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Hm, they're here for me now, again. Either (1) he moved them to a better host, or (2) the host is just unreliable and goes down at various times / has issues with its CDN that mean it works for some locations but not others. Leaning towards (2), as as far as I can tell from the Wayback post, the hos ...
written 3 months ago by Isaac Joseph80
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Images are gone for me, too, FWIW. Resorting to [Wayback Machine](https://web.archive.org/web/20160609152315/https://www.biostars.org/p/84686/). ...
written 4 months ago by Isaac Joseph80
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Answer: A: MAPping Quality v.s. Alignment Score (AS) in SAM format
... For posterity (and to save you a click to SEQAnswers and parsing its rambling, old-style forum interface), the helpful bit for me was: @xiangwulu: > Alignment score is a metric > that tells you how similar the read is to the reference. AS increases > with the number of matches and decrease ...
written 5 months ago by Isaac Joseph80
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Answer: A: Getting Allele Frequencies From 1000 Genomes
... Here's an example programmatically, using `python` and the handy-dandy [`myvariant`][1] package (thanks [Cyrus Afrasiabi][2], [Chunlei Wu][3]): import myvariant myvariant.MyVariantInfo() mv.query('dbsnp.rsid:rs58991260', fields='dbsnp')['hits'][0]['dbsnp']['gmaf'] # returns 0.02157 Not ...
written 17 months ago by Isaac Joseph80
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Comment: C: How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
... Plot twist: said posterity now includes me, as I forgot how to do this, and moreover, forgot that I knew how to do this, so Google®ed it and came upon this question again. ...
written 20 months ago by Isaac Joseph80
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Comment: C: Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File
... `samtools view` expands the huge `.bam` file though. That does, however, save hard disk space. ...
written 22 months ago by Isaac Joseph80
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Answer: A: How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
... So, for posterity, to save time and do something roughly equivalent, just do `biocLite('FDb.InfiniumMethylation.hg19')`instead of the above. Details: the above appears to be deprecated; I received the following error: >biocLite("IlluminaHumanMethylation450k.db") ... Error : . ...
written 22 months ago by Isaac Joseph80
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Comment: C: How To Get Number Of Reads In Bam File Efficiently In Python?
... Unfortunately, that prints the number of alignments in the file, which can be (and usually is) distinct from the number of reads (because each read can align more than once).  ...
written 3.1 years ago by Isaac Joseph80
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Comment: C: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
... I agree with this notion in general, but I'm seriously chafing at the (in my opinion) still quite derogatory and insulting articulation above, Pierre. I'm also chafing at the one-dimensionality that such a badge labeling system implies. Perhaps we should have several categories - *-seq skills/know ...
written 5.2 years ago by Isaac Joseph80
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Comment: C: Does Samtools Tview Hide Pcr And Optical Duplicates?
... I suppose there's no known way to get it to stop hiding such reads? (Perhaps something inherited from pileup syntax?) ...
written 5.2 years ago by Isaac Joseph80

Latest awards to Isaac Joseph

Epic Question 4 months ago, created a question with more than 10,000 views. For Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File
Supporter 17 months ago, voted at least 25 times.
Great Question 2.8 years ago, created a question with more than 5,000 views. For Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Length Of Read Needed To Confidently Map Sequence
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.

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