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Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
18,930
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
10 years, 5 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 • 959 results • page 1 of 96 • next >
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Answer: A: Reads That Are Used In De Novo Assemblies That Did Not Map To Contigs
... Any read that spans two contigs won't map to any one contig, although the kmers that make up that read are still "used". You might ask "why there are multiple contigs at all when there are reads that could connect them?" The answer is that those reads in fact map to *multiple* contigs because of re ...
written 4 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Basic Bam File Annotation
... https://github.com/databio/GenomicDistributions might be worth adding here ...
written 10 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake: How to handle dynamically created files with dynamically created file
... oh I was totally unaware of checkpoints and must have just ignored that - that's new. very cool. ...
written 14 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake: How to handle dynamically created files with dynamically created file
... i mean run your rule finished should glob those fa's and generate the corresponding tsv's rule finished: input: tsvlist = [os.path.basename(fa)+'.tsv' for f in glob.glob('no_BL62_hits/*')] ...
written 15 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake: How to handle dynamically created files with dynamically created file
... you can try the new `dynamic` operator in Snakemake but it might be easier to have an intermediate target (fasta_expansion.done) and a final target that uses `glob.glob('no_BL62_hits/*')` to see which files exist in no_BL62_hits. Then run the targets sequentially `Snakemake fasta_expansion.done & ...
written 16 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Snakemake: How to handle dynamically created files with dynamically created file
... these don't really sound dynamically-created in the sense you have no idea what they'll be called - don't they simply correspond to the deflines in your fasta file? Then you can derive that target from a function that reads the deflines and transforms them into .tsv's (https://www.biostars.org/p/710 ...
written 17 days ago by Jeremy Leipzig ♦ 19k
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Answer: A: Snakemake: How to handle dynamically created files with dynamically created file
... Write a function to return your targets from your `DE.faa`. Go ahead and evaluate it up top and assign a variable to its output, use that as the target to `aggregate`. You can't expect `aggregate_input` to somehow know what the wildcards are from another unrelated rule. All your `touch` commands b ...
written 20 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Difference between "cross-ancestry" and "trans-ethnic"
... this paper https://www.nature.com/articles/s41588-018-0303-9 uses trans-ethnic to refer to self-reported races like whites, blacks, Hispanics, Asians, Native Americans and trans-ancestry to refer to populations like European, African, East Asian and South Asian ...
written 23 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Is MAPQ score related to Phred quality score?
... You can certainly try that but it might actually make your results worse. Most aligners are already quality-aware. ...
written 26 days ago by Jeremy Leipzig ♦ 19k
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Comment: C: Is MAPQ score related to Phred quality score?
... No Phred refers to bases and MAPQ refers to the alignment. You can do a QC step such as filtering and trimming reads, but that practice is less popular than it used to be. ...
written 27 days ago by Jeremy Leipzig ♦ 19k

Latest awards to Jeremy Leipzig

Teacher 19 days ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 7 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Popular Question 8 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Great Question 9 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 10 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: 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
Teacher 11 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
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Great Question 13 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 14 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Popular Question 14 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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