Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 17k
- Reputation:
- 17,250
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- Location:
- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
- Twitter:
- jermdemo
- Scholar ID:
- Google Scholar Page
- Last seen:
- 14 hours ago
- Joined:
- 8 years, 3 months ago
- Email:
- l******@gmail.com
I am a bioinformatics software developer known mostly for my posts on big-ass servers, damn microarray papers, and the reproducible research guilt trip, as well as my review of pipeline frameworks. I have worked in virology, crop genomics, and on various pediatric diseases as a programmer, analyst, and architect. I'm currently a PhD student at Drexel.
Posts by Jeremy Leipzig
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... Usually the caller has no idea which chromosome homolog a variant is on. It can just see variants that are in the same read or read pair (unlikely for short reads) or it can try to infer which variants are on the same chromosome homolog (phased) using read-backed phasing (as part of the read assembl ...
written 15 days ago by
Jeremy Leipzig ♦ 17k
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... TIL: UMIs are "unique molecular identifiers", more widely known as barcodes ...
written 24 days ago by
Jeremy Leipzig ♦ 17k
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Comment:
C: TMB Tumor Mutation Burden
... I think they sequence to ridiculously high median depth (500X) so they might have started to saturate by then?
That having been said it's a crude metric for 2018 to say the least. I'm surprised it even has a name. ...
written 4 weeks ago by
Jeremy Leipzig ♦ 17k
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Comment:
C: Workflows! Where is the code?
... That sounds about right.
I'm using the term "configuration" to describe configuration-based (using a specification markup language) rather than convention-based DSLs:
https://academic.oup.com/bib/article/18/3/530/2562749 ...
written 5 weeks ago by
Jeremy Leipzig ♦ 17k
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Answer:
A: Workflows! Where is the code?
... CWL and WDL are specifications for configuration-based pipeline frameworks. These don't allow a lot of inline code, unlike domain specific languages. ...
written 5 weeks ago by
Jeremy Leipzig ♦ 17k
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... > "my laptop"
who told you that was an acceptable platform? ...
written 5 weeks ago by
Jeremy Leipzig ♦ 17k
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... "fold change" is a bad metric and also the term itself can be ambiguous when speaking to different people, as evidenced by the confused entry in wikipedia
https://en.wikipedia.org/wiki/Fold_change
"log2 fold change" is symmetric and unambiguous ...
written 7 weeks ago by
Jeremy Leipzig ♦ 17k
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Comment:
C: New to bioinformatics.....
... "What my team has developed under my expert leadership is a comprehensive solution for data-driven predictive personalized medicine and cost savings. Big Data. IoT." ...
written 12 weeks ago by
Jeremy Leipzig ♦ 17k
3
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501
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Comment:
C: New to bioinformatics.....
... Nonsense, this guy is executive material. He'll be my boss someday. ...
written 12 weeks ago by
Jeremy Leipzig ♦ 17k
0
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501
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Comment:
C: New to bioinformatics.....
... Most of the bigger SaaS players (e.g. SBG, DNANexus) have taken a different approach than selling "we can make your analysis easy" to every PI and have made most of their money through partnerships either with government or pharma. ...
written 12 weeks ago by
Jeremy Leipzig ♦ 17k
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For C: Big Ass Servers & Storage
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For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
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For C: Big Ass Servers & Storage
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