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Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
18,480
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
9 years, 10 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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Comment: C: Event-based software for alternative splicing with three conditions?
... that's an interesting point. ANOVAs became popular before computers, and they require a two-way post-hoc anyway. The majority of efforts in differential expression are two-way, so it's no surprise differential splicing would be the same. Granted you are introducing some multiple testing issues when ...
written 1 day ago by Jeremy Leipzig ♦ 18k
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Comment: C: Event-based software for alternative splicing with three conditions?
... i'm not so sure software that handles 3 conditions is really much better than A vs B and A vs C and B vs C ...
written 2 days ago by Jeremy Leipzig ♦ 18k
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Comment: C: Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?
... try `prcomp` with `scale=TRUE` ...
written 8 days ago by Jeremy Leipzig ♦ 18k
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Answer: A: Computational resources for WGS variant calling
... you have enough memory (GATK 3.X might take 64GB for some steps). In theory, you might finish this in 12 days or so. The local storage for scratch space might be an issue, maybe 50GB is a typo? My phone has more than that. Perhaps, more importantly, is that you bring an experienced bioinformatics ...
written 8 days ago by Jeremy Leipzig ♦ 18k
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Answer: A: GWAS summary statistics
... GWAS summary statistics refer to supplying three important pieces of information: SNP, Phenotype, and P-value This differs from full GWAS data which would have calls for every individual at every SNP Here are the fields and an entry from the NHGRI-EBI GWAS Catalog: DATE ADDED TO CATALOG P ...
written 13 days ago by Jeremy Leipzig ♦ 18k
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Comment: C: Seqlogo generation and interpretation
... in this case seqlogo is just the CLI version of weblogo. they should be identical given the same parameters and input. ...
written 4 weeks ago by Jeremy Leipzig ♦ 18k
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Answer: A: Seqlogo generation and interpretation
... This is what I got using seqlogo from weblogo.2.8.2 your fasta file. Could you be just looking at the wrong output file from a previous run? ![enter image description here][1] [1]: https://i.ibb.co/XxrcWyK/Screen-Shot-2019-12-19-at-1-27-04-PM.png ...
written 4 weeks ago by Jeremy Leipzig ♦ 18k
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Comment: C: Seqlogo generation and interpretation
... show us the nucleotide matrix you fed seqlogo ...
written 4 weeks ago by Jeremy Leipzig ♦ 18k
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Answer: A: How download FDA approved drug database?
... https://www.drugbank.ca/releases/latest there are fields in drugbank that distinguish approved drugs from investigational or experimental ones ...
written 10 weeks ago by Jeremy Leipzig ♦ 18k
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Comment: C: snakemake: pipeline failed with MissingOutputException
... The way to debug anything is to start with something that works and then make small changes until it doesn’t. I am not totally convinced your worker nodes have access to /work. Maybe drop the absolute directories and try some helloworld Snakefiles with qsub and work your way up to the problem. ...
written 10 weeks ago by Jeremy Leipzig ♦ 18k

Latest awards to Jeremy Leipzig

Scholar 16 days ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Great Question 3 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Great Question 7 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 7 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Popular Question 8 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?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 10 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 10 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 11 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 12 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?
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