Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
18,130
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
9 years, 3 months ago
Email:
l******@gmail.com

I am a bioinformatics software developer known mostly for my posts on big-ass serversdamn 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

<prev • 880 results • page 1 of 88 • next >
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Comment: C: How to get nuclear and mitochondrial gene sequences ?
... This question is phrased too vaguely to know what your problem actually is. The vast majority of genes are nuclear so why would you have trouble with those? Are you talking about NUMTs? How about you rephrase your question to fetching a specific gene and we'll show you how to do it? ...
written 1 day ago by Jeremy Leipzig18k
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Answer: A: Prevalence of genetic disorders
... https://github.com/Orphanet/Orphadata.org has prevelance data on 9355 rare diseases ...
written 4 days ago by Jeremy Leipzig18k
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Comment: C: Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
... Accepted. PubPeer has lasted the test of time. ...
written 6 days ago by Jeremy Leipzig18k
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Comment: C: snakemake wildcard for fastq files
... you need to follow up on your older questions first. you keep posting variations of the same problem without resolving earlier issues. ...
written 17 days ago by Jeremy Leipzig18k
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Comment: C: Snakemake, config .yaml
... start with a one-line config. add lines until the offender shows up. ...
written 19 days ago by Jeremy Leipzig18k
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Answer: A: When will the HG 19/ GRC37 finally become obsolete
... i wouldn't hold your breath Pubmed central full-text searches e.g. https://www.ncbi.nlm.nih.gov/pmc/?term=((%222015%22%5BElectronic+Publication+Date%5D+%3A+%222015%22%5BElectronic+Publication+Date%5D))+AND+grch37%5BText+Word%5D hg38 hg19 grch37 grch38 2019 279 105 ...
written 24 days ago by Jeremy Leipzig18k
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Comment: C: Appropriate use of wildcards for single instances in Snakemake
... That shouldn't be happening. Try listing a couple of target files explicitly. "garfield_output/ATAC/chr1/garfield.prep.adhd.out","garfield_output/ATAC/chr2/garfield.prep.adhd.out" ...
written 24 days ago by Jeremy Leipzig18k
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Answer: A: Appropriate use of wildcards for single instances in Snakemake
... The only way Snakemake can tell which CHR you want in input is if you request it as output, so your wildcard rule needs to produce a CHR-specific output. Any wildcard in the input needs to be in the output, although the reverse isn't necessarily true. output: "garfield_output/{ANN}/chr{ ...
written 25 days ago by Jeremy Leipzig18k
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Comment: C: How do I get the reference allele from this Ensembl variation endpoint?
... Right so how do I know *consistently* that it’s `T` ...
written 27 days ago by Jeremy Leipzig18k
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How do I get the reference allele from this Ensembl variation endpoint?
... Looking at: https://rest.ensembl.org/documentation/info/variation_id is there a consistent way to tell what the reference allele is? ...
ensembl written 27 days ago by Jeremy Leipzig18k

Latest awards to Jeremy Leipzig

Great Question 7 days ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Popular Question 28 days ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Great Question 3 months ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Great Question 5 months ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 11 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Student 11 months ago, asked a question with at least 3 up-votes. For What are the best examples of sample naming conventions?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Popular Question 12 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Epic Question 13 months ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp

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