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Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
19,300
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
1 day, 7 hours ago
Joined:
10 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

<prev • 1,002 results • page 1 of 101 • next >
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Comment: C: How to download triple negative breast cancer RNA-seq fpkm data from GDC.
... saw this post mentioned in a DNANexus tutorial https://www.youtube.com/watch?v=1TcvCrszprk ...
written 3 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: What does p-value mean ? What and how can i interpret the results
... I find this just as succinct and less easily misinterpreted: The p-value is the probability that random chance could produce the observed difference ...
written 9 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: GWAS summary statistics
... please post a new Biostars question ...
written 9 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Specific question on torturing the data until it confesses
... I'm not sure what different models are being used to generate different lists of DE genes, but every time you do that you'd have to correct for multiple testing, even at the enrichment stage ...
written 27 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: RNA-Seq junction reads overhang imbalance
... thanks for uploading this. I must say I am stumped. It does look like the overhang alignments are stopping at a particular base pair position as though there is an N in the reference that is causing a soft clip. ...
written 6 weeks ago by Jeremy Leipzig ♦ 19k
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Comment: C: RNA-Seq junction reads overhang imbalance
... can you provide an IGV screenshot of this? ...
written 6 weeks ago by Jeremy Leipzig ♦ 19k
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Comment: C: pipeline for variant discovery in target resequencing
... well if the duplicates are based on PCR then I'm not sure why you would say using amplicons would negate that. At any rate for variant calling I doubt removing duplicates would make a huge difference unless a sizeable proportion of duplicates were of such low quality they were leading to a variant n ...
written 6 weeks ago by Jeremy Leipzig ♦ 19k
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Comment: C: How to call denovo and rare variants from a trios cohort?
... a gVCF can only handle one individual, so you couldn't use them call trios with tools that expect a trio VCF (correction: yes there are multi-sample gVCFs that briefly arise from CombineGVCFs but they are never found in the wild) ...
written 6 weeks ago by Jeremy Leipzig ♦ 19k
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Answer: A: How to call denovo and rare variants from a trios cohort?
... You'll need a VCF with the trio(s), not 45 gVCFs, so GenotypeGVCFs those together (or at least into 15 trio vcfs) Annotate with [snpEff][1] java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.69 trio.vcf > trio_snpeff.vcf and then to get variant frequencies, annotate with gnomAD using VCFanno ...
written 7 weeks ago by Jeremy Leipzig ♦ 19k
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Answer: A: Calculating minor allele frequency for GnomAD VCF file
... Yes AF is the MAF here. It bears mentioning that sometimes the variant might not necessarily be the less common allele in all populations, and the major allele might even confer something weakly deleterious. But in these two cases, they only saw one individual with this mutation. ...
written 8 weeks ago by Jeremy Leipzig ♦ 19k

Latest awards to Jeremy Leipzig

Great Question 7 weeks ago, created a question with more than 5,000 views. For What Is The Expected Size Of A Whole Genome Vcf And Bcf?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Oracle 8 weeks ago, created more than 1,000 posts (questions + answers + comments).
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?
Popular Question 4 months ago, created a question with more than 1,000 views. For Did dbSNP not get the memo about hg38 chromosome names?
Great Question 4 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?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 4 months ago, created a question with more than 1,000 views. For Did dbSNP not get the memo about hg38 chromosome names?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 11 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 13 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Popular Question 14 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Great Question 15 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
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