Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
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Philadelphia, PA
Website:
http://jermdemo.blogsp...
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jermdemo
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Last seen:
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10 years, 3 months ago
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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 • 936 results • page 2 of 94 • next >
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... don't use expand in wildcard rules ...
written 4 days ago by Jeremy Leipzig19k
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... ok there's many ways to skin a cat but this is one strategy: `def getHome(sample): return(os.path.join(dict(samples_set)[sample],"{0}_{1}.fastq.gz".format(sample,pair)) for pair in ['R1','R2'])` `r1 = lambda wildcards: getHome(wildcards.sample)[0],` `r2 = lambda wildcards: getHome(wildcards.samp ...
written 4 days ago by Jeremy Leipzig19k
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... ok yes you can prepend your input with directories i.e `r1 = os.path.join(FASTQ_DIR,"{sample}_R1.fastq.gz")`. that's ok i would just avoid `expand` in wildcards rules. now for the zip thing you are close. you can just use `samples_set` to create a lookup function `def getHome(sample): return(os.pat ...
written 8 days ago by Jeremy Leipzig19k
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Answer: A: creating container - should it contain a workflow manager?
... These (Docker/Bash/Pipeline frameworks) are compatible, not mutually exclusive, technologies. Pipeline frameworks offer: - Parameterization - File/task abstraction and dependency graphs - Reentrancy You can definitely re-invent the wheel but, as you have noted, it gets ugly real fast ...
written 8 days ago by Jeremy Leipzig19k
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Answer: A: Using wildcards to accept paired-end reads from Snakemake
... OK lemme break this down into three four heuristics (conveniently numbered 1, 1, 1, and 2) 1. Keep your implicit wildcard rules as simple as possible. Describe what they do - no more, no less. There is generally no need for `expand` in these as far as samples go. `expand` will collide with wildcard ...
written 8 days ago by Jeremy Leipzig19k
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Comment: C: Versioning of Blast DB and Reproducible Research
... when did the OP mention `nt` or `nr`? ...
written 8 days ago by Jeremy Leipzig19k
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Answer: A: Versioning of Blast DB and Reproducible Research
... I think the problem here is that the BLAST database file is monolithic, which makes daily versioning too disk space intensive. The good news is that the FASTA files that are indexed by BLAST are "atomic". So all you really need is a reliable recipe to recreate a database from a subset of date-stampe ...
written 8 days ago by Jeremy Leipzig19k
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Answer: A: Generalizing snakemake MACS2 code - WildcardError Wildcards in input files canno
... First, the "{sample}" wildcards don't exist outside of rules. You can pass wildcards to functions (`def myfunction(wildcardsGoHereReadTheDocs)`) but that is for functions where the input depends on the wildcards. Second, you're making this more complicated than it has to be. `peakcaller` *does* exi ...
written 10 days ago by Jeremy Leipzig19k
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Comment: C: Order assignment given family and genus level in R
... ok give us the name of a family you are working with ...
written 11 days ago by Jeremy Leipzig19k
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Comment: C: Order assignment given family and genus level in R
... The `taxize` package has a number of tools to query various phylogenies. Can you provide an example of a family/genus/species for which you would like the order? ...
written 11 days ago by Jeremy Leipzig19k

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Appreciated 3 days ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
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?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
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Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 8 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 ?
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Great Question 11 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 12 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Popular Question 12 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?
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?

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