Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 17k
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- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
- Twitter:
- jermdemo
- Scholar ID:
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- Last seen:
- 6 hours ago
- Joined:
- 8 years, 7 months ago
- Email:
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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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... Dr. Yi Xing’s lab (https://xinglab.org/) at the Children’s Hospital of Philadelphia (CHOP) and the University of Pennsylvania (Penn) has multiple openings for Bioinformatics Data Scientist or Postdoctoral Fellow. Our lab is broadly interested in computational biology and genomics of RNA processing a ...
written 1 day ago by
Jeremy Leipzig ♦ 17k
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... this is a nim solution
import strutils
var
line: string
seqCnt = 0
charCnt = 0
proc main()=
for line in stdin.lines:
if line.startsWith('>'):
inc seqCnt
else:
charCnt += len(line)
echo (charCnt/seqCnt)
ma ...
written 15 days ago by
Jeremy Leipzig ♦ 17k
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... Is there a package that takes a phylogenetic tree and allows you to specify fixed and random effects by specifying a level of the tree, so everything above is random and everything below is fixed (or vice-versa)?
So if you have a homologous SNP in some distant species and some phenotypic measure, y ...
written 16 days ago by
Jeremy Leipzig ♦ 17k
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128
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... it is a custom array derived from some freeze of a genome ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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... right this is a complete mystery, so I need a very sparse gappy aligner or something that can take a list of chromosomal coordinates and extract the sequences from every genome on earth ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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128
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... I only have the SNPs that the probes interrogate, not the actual probe sequences ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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... Let's say you were given a microarray probeset, consisting of sparsely scattered SNPs of Allele A and B. If you didn't know from which genome or freeze it was derived, how would you find out? ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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... 1. Your estimates should be derived from empirical evidence. SGE has `qacct` which should tell you how much memory was consumed at peak for a completed process.
2. A memory-bound process can certainly be slowed by lack of memory, but it's more likely to just crash. Computers are great at managing li ...
written 7 weeks ago by
Jeremy Leipzig ♦ 17k
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... I'm interested in finding all recent (>=2017/01/01) papers with at least 5 citations and open associated SRA data in Entrez. Can someone provide an automated strategy for this? ...
written 12 weeks ago by
Jeremy Leipzig ♦ 17k
3
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240
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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 4 months ago by
Jeremy Leipzig ♦ 17k
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6 months ago,
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For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
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For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
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