Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
16,430
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Scholar ID:
Google Scholar Page
Last seen:
2 days, 1 hour ago
Joined:
7 years, 1 month ago
Email:
l******@gmail.com

Bioinformatics software developer working at a pediatric hospital.

Posts by Jeremy Leipzig

<prev • 767 results • page 1 of 77 • next >
0
votes
1
answer
93
views
1
answers
Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... show us one that's missing ...
written 5 days ago by Jeremy Leipzig16k
0
votes
0
answers
71
views
0
answers
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 5 days ago by Jeremy Leipzig16k
2
votes
2
answers
108
views
2
answers
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 6 days ago by Jeremy Leipzig16k
5
votes
7
answers
1.3k
views
7
answers
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 9 days ago by Jeremy Leipzig16k
1
vote
1
answer
209
views
1
answers
Comment: C: GWAS & Logistic regression in R
... It's probably still ok to use GAPIT for this, you just have to round the responses to 0 or 1, assuming these responses are ordered in some meaningful way ...
written 7 weeks ago by Jeremy Leipzig16k
0
votes
1
answer
209
views
1
answers
Comment: C: GWAS & Logistic regression in R
... Is it continuous? ...
written 7 weeks ago by Jeremy Leipzig16k
1
vote
2
answers
913
views
2
answers
Comment: C: mitochondrial blacklists ATAC-Seq
... real NUMTs, assuming transposase binds to them, would map to the NUMT regions you list above. I don't know whether they would also align to chrM. Better to blacklist both chrM and the regions. ...
written 7 weeks ago by Jeremy Leipzig16k
1
vote
2
answers
913
views
2
answers
Comment: C: mitochondrial blacklists ATAC-Seq
... These homologous regions are called NUMTs ...
written 8 weeks ago by Jeremy Leipzig16k
0
votes
1
answer
209
views
1
answers
Answer: A: GWAS & Logistic regression in R
... A logistic regression is where your dependent, outcome variable is dichotomous or binary (aka logical). GAPIT is a mixed model linear regression, which means it tries to divide the regressors into fixed and random effects. This is super important in agriculture where most of all the GWAS signals en ...
written 8 weeks ago by Jeremy Leipzig16k
0
votes
0
answers
279
views
0
answers
Comment: C: hppRNA: a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of
... do you have something against github or even bitbucket? sourceforge is a ghost town ...
written 3 months ago by Jeremy Leipzig16k

Latest awards to Jeremy Leipzig

Appreciated 4 days ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
Great Question 4 weeks ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Epic Question 4 weeks ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
Popular Question 6 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?
Great Question 6 weeks 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 11 weeks 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 12 weeks 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 3 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 4 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Student 4 months ago, asked a question with at least 3 up-votes. For Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?
Teacher 6 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 7 months ago, created an answer that was upvoted at least 5 times. For A: Making bioinformatics help and tutorials open
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 7 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?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Why Does Rna-Seq Read Count Fit Poisson Distribution?
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Prophet 9 months ago, created a post with more than 20 followers. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Popular Question 9 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Popular Question 10 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 11 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Appreciated 11 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: No Reads Ever Map To First 3Million Bases Of Chromosomes In Mouse Genome! Why?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 714 users visited in the last hour