Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
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Last seen:
2 hours ago
Joined:
7 years, 5 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 • 773 results • page 1 of 78 • next >
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Comment: C: How to handle metadata in bioinformatics pipelines?
... yes nice support for ontologies to define input/output formats in CWL https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/tools/fastq_to_fasta.cwl cwlVersion: v1.0 class: CommandLineTool hints: - class: SoftwareRequirement packages: biopytho ...
written 20 days ago by Jeremy Leipzig17k
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Answer: A: Rare Variant Association Tests and ExAC Data Set
... ![http://i.imgur.com/IAYtE2il.png][1] [1]: http://i.imgur.com/IAYtE2il.png ...
written 9 weeks ago by Jeremy Leipzig17k
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Comment: C: is seqanswers.com down?
... Hello mjp! We believe that this post does not fit the main topic of this site. off-topic For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be happy to ...
written 10 weeks ago by Jeremy Leipzig17k
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Comment: C: is seqanswers.com down?
... https://twitter.com/SEQanswers/status/864165020669587456 ...
written 10 weeks ago by Jeremy Leipzig17k
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Answer: A: IndelRealign mitochondrial DNA using b37
... The problem is likely naming related (M vs MT) but the bigger issue is that this GATK realignment approach is really overkill for mitochondria sequences. You could easily do a real alignment using BLAST or something else more sensitive. There are no mitochondrial gold standard indels in your referen ...
written 12 weeks ago by Jeremy Leipzig17k
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Comment: C: How to get VCF file into a data matrix form for machine-learning? (new to vcf fi
... see https://www.biostars.org/p/77840/ ...
written 3 months ago by Jeremy Leipzig17k
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... show us one that's missing ...
written 3 months ago by Jeremy Leipzig17k
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Which sequencing services provide the highest quality metadata
... Which sequencing labs have the highest standards in terms of providing wet lab protocols and bioinformatic metadata? This is our wishlist of sequence metadata - we wouldn't expect all this but more than a sequence file on a thumb drive: adapter_name adapter_sequence aliquots ...
metadata written 3 months ago by Jeremy Leipzig17k
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Answer: A: How to call mitochondrial SNP?
... I take it you have aligned your sequences to rCRS and you have a .bam file? You can submit that to Haplogrep. You can also call the consensus sequence using samtools, which will yield a fasta you can submit to Mitomaster. https://www.biostars.org/p/178510/ ...
written 3 months ago by Jeremy Leipzig17k
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Comment: C: StackExchange/Area51 bioinformatics is back
... Yes, the most useful questions on SE tend to be off-topic and under threat by the rigid Asperger people who run those sites. ...
written 3 months ago by Jeremy Leipzig17k

Latest awards to Jeremy Leipzig

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 7 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?
Prophet 9 weeks ago, created a post with more than 20 followers. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Autobiographer 10 weeks ago, has more than 80 characters in the information field of the user's profile.
Good Question 12 weeks ago, asked a question that was upvoted at least 5 times. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
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?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 3 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?
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
Great Question 4 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Epic Question 4 months ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
Popular Question 5 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?
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?
Great Question 6 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?
Good Answer 6 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 6 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Student 8 months ago, asked a question with at least 3 up-votes. For Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?
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?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Making bioinformatics help and tutorials open
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
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?

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