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Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
18,580
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
10 years, 1 month 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 • 914 results • page 1 of 92 • next >
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Answer: A: likelihood of number of consecutive Ns in miRNA sequence
... this should be as simple as downloading the hairpins or mature sequences and looking for your patterns perl -ne '$x=5;if(/>/){if ($seq){$seq =~ m/((A{$x,}|C{$x,}|G{$x,}|U{$x,}))/ && print $def.$1."\n";}$seq="";$def=$_;}else{chomp;$seq=$seq.$_;}' hairpin.fa >cel-mir-38 MI00000 ...
written 6 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: likelihood of number of consecutive Ns in miRNA sequence
... I think the OP means any mononucleotide kmer? ...
written 6 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake Error (incorrect wildcard use)
... in snakemake you provide a recipe for making a target, but then you have to actually ask for the target. You can even ask on the command line but it's preferable to set a target rule as cschu181 suggested. ...
written 6 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Strange coverage of mtDNA - need help interpreting MiSeq results
... Looking at the BAM may be too late to diagnose what is happening. I would start by grepping your raw reads for mtDNA sequence around that 3234 area - agatggc, not much longer than that. https://www.mitomap.org/foswiki/bin/view/MITOMAP/HumanMitoSeq If they don't even exist you know it's something i ...
written 5 weeks ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake - parameter file treated as a wildcard
... somehow Snakemake is thinking your BLACKLIST path is relative instead of absolute. When you run Snakemake are you using some working directory argument? If you are desperate maybe symlink your /mnt/data/ directory to your working directory and stop using absolute paths. ...
written 8 weeks ago by Jeremy Leipzig ♦ 19k
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Comment: C: Adding wildcards in Snakemake rule
... well I'm not crazy about you using underscores in both the sample names and as delimiters. try using a delimiter that won't confuse the regex. also just update your original question, you don't need to submit an answer. ...
written 9 weeks ago by Jeremy Leipzig ♦ 19k
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Answer: A: Adding wildcards in Snakemake rule
... OK the wildcard rules look fine, now create a target rule to produce the files you want rule mytargetrule: input: "results/mysample/fasta/mysample_bwa_hg37_qfilt.fa", "results/mysample/fasta/mysample_bwa_hg37_qfiltreg.fa" ...
written 9 weeks ago by Jeremy Leipzig ♦ 19k
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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 10 weeks ago by Jeremy Leipzig ♦ 19k
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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 11 weeks ago by Jeremy Leipzig ♦ 19k
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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 11 weeks ago by Jeremy Leipzig ♦ 19k

Latest awards to Jeremy Leipzig

Teacher 21 days ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 3 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Popular Question 4 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Great Question 5 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Scholar 6 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 6 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: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Great Question 9 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 10 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Popular Question 10 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 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?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 13 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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