The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
As a group working on #scRNA-seq and #snRNA-seq analysis, we’ve noticed that certain popular and publicly-available datasets, e.g. the PBMC datasets from 10x Genomics, are used repeatedly for tutorials, method development, etc. and often reprocessed. 1/🧵
— Rob Patro (@nomad421) May 6, 2022
As a group working on #scRNA-seq and #snRNA-seq analysis, we’ve noticed that certain popular and publicly-available datasets, e.g. the PBMC datasets from 10x Genomics, are used repeatedly for tutorials, method development, etc. and often reprocessed. 1/🧵
— Rob Patro (@nomad421) May 6, 2022submitted by: Istvan Albert
(2/9) How often have you wanted to find sequencing data for your PI only to be met with a collection of incomprehensible “GEO” accessions for raw data stored in the “SRA”? We built `ffq` to solve this problem. https://t.co/q37gN4Gwrw pic.twitter.com/ldqy0fxfBV
— Angel Galvez Merchan (@agalvezmerchan) May 5, 2022
(2/9) How often have you wanted to find sequencing data for your PI only to be met with a collection of incomprehensible “GEO” accessions for raw data stored in the “SRA”? We built `ffq` to solve this problem. https://t.co/q37gN4Gwrw pic.twitter.com/ldqy0fxfBV
— Angel Galvez Merchan (@agalvezmerchan) May 5, 2022submitted by: Istvan Albert
New Science's Report on the NIH - New Science (newscience.org)
In this analysis from New Science, writer Matt Faherty synthesizes dozens of interviews with current and former NIH employees and grant recipients, as well as hundreds of documents from the academic literature, to provide a comprehensive, but non-exhaustive, overview of the NIH’s operations and impact on bioscience research.
Our findings are complex and laden with opposing truths: Yes, the NIH has been the main driver of bioscience innovation for more than 80 years. Without the hundreds of billions of dollars that the NIH has allocated to U.S. scientists, the world, perhaps, would not have CRISPR gene-editing technologies or modern CAR-T therapies to treat cancer. But the NIH, like all giant bureaucracies, suffers from structural problems that hinder its efficiency and leads to considerable, wasteful spending. The agency is risk-averse and excessively funds an aging cadre of scientists, likely at the cost of losing young scientists and missing out on ambitious, transformative ideas.
submitted by: Istvan Albert
The journey to a paper is sometimes long and windy!
Let's look at how we got to our latest preprint!
— Mick W@tson (@BioMickWatson) May 3, 2022
The journey to a paper is sometimes long and windy!
Let's look at how we got to our latest preprint!
submitted by: Istvan Albert
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure | BMC Bioinformatics | Full Text (bmcbioinformatics.biomedcentral.com)
GEMmaker, is a nf-core compliant, Nextflow workflow, that quantifies gene expression from small to massive RNA-seq datasets. GEMmaker ensures results are highly reproducible through the use of versioned containerized software that can be executed on a single workstation, institutional compute cluster, Kubernetes platform or the cloud. GEMmaker supports popular alignment and quantification tools providing results in raw and normalized formats. GEMmaker is unique in that it can scale to process thousands of local or remote stored samples without exceeding available data storage.
submitted by: Istvan Albert
Variant normalization is a perennial problem in genomics. Should we shift indels left, or right? How big should our variant calls be (SNPs vs. MNPs vs. complex alleles)...? pic.twitter.com/RlssdyoGCE
— Erik Garrison (@erikgarrison) May 2, 2022
Variant normalization is a perennial problem in genomics. Should we shift indels left, or right? How big should our variant calls be (SNPs vs. MNPs vs. complex alleles)...? pic.twitter.com/RlssdyoGCE
— Erik Garrison (@erikgarrison) May 2, 2022submitted by: Istvan Albert
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