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Sol Shenker

@seqcmd.bsky.social

Scientist, Bioinformatics, cancer

Sol Shenker @seqcmd.bsky.social · 21/05/2025

Does it help to have them "check each other's work"? Eg, run it with two different tools, if you get the same result there's a higher chance it's right? Or there's something about how the PDF is typeset that makes some sequences particularly hard to extract correctly?

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Sol Shenker @seqcmd.bsky.social · 08/12/2024

If you're willing to try nextflow instead of snakemake I put together a generic module for split-apply-combine that can be used to easily parallelize single-threaded FASTQ processing programs. You just need to write a little wrapper process, and specify fan-out number github.com/shenkers/nf-...

github.com

GitHub - shenkers/nf-scatter-gather: A modular nextflow construct for parallelizing simple FASTQ processing tasks with map/reduce

A modular nextflow construct for parallelizing simple FASTQ processing tasks with map/reduce - shenkers/nf-scatter-gather

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Sol Shenker @seqcmd.bsky.social · 04/02/2024

Wow, cool resource to study DDR! www.nature.com/articles/s41...

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Sol Shenker @seqcmd.bsky.social · 29/09/2023

Bouillon Bilk, it was very cool!

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Sol Shenker @seqcmd.bsky.social · 26/09/2023

Impressive speedup! It's the same fundamental data-structures, it's just faster because it's written in Rust? Haven't used rust for anything yet, but I would have expected performance to be pretty similar to bedtool's cpp.

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Sol Shenker @seqcmd.bsky.social · 19/09/2023

Why do you think that is? Are we measuring the wrong thing? We are measuring the right thing, but we don't know how to interpret it? Something else?

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Sol Shenker @seqcmd.bsky.social · 15/09/2023

Is that an individual knockout performed in adult mice? Is it a failure to develop testes vs failure of germ stem cells to differentiate? If you subsequently turn it back on is fertility restored?

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Sol Shenker @seqcmd.bsky.social · 14/09/2023

@chrisamiller.bsky.social @lwpembleton.bsky.social I'm trying to bootstrap a platform exactly along these lines, hoping to help small strappy companies or research labs. Would love show and hear more about your pain points if you have time.

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