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Lior Pachter Profile picture
@lpachter
Aug 11, 2020 • 4 tweets • 3 min read • Read on X
I was excited to read this new preprint on #covid19 testing using NGS until I read the data and code availability section: "NGS data, as well as sample sheets and results are available under request."

This is unacceptable.

Consider these two recent #SwabSeq preprints: medrxiv.org/content/10.110…

medrxiv.org/content/10.110…

Both were published with data as well as open source code and protocols making everything fully reproducible and usable.
Yet many groups continue to insist that it's ok to keep data and code locked away (and come up with all sorts of BS reasons to justify their stonewalling).
I get it. People want to make money from #covid19 testing. But right now this BS is slowing down the roll out of low-cost, scalable, technologies. There are many reasons why testing is broken in the US and this is not the only reason but it is a reason.
liorpachter.wordpress.com/2020/07/31/how…

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More from @lpachter

Lior Pachter Profile picture
Jul 20
The mantra that spatial transcriptomics is about location, location, location is catchy, but what does it really mean? We have just posted , work of Kayla Jackson et al., that describes the concordex method for identifying spatial homogeneous regions. 1/🧵biorxiv.org/content/10.110…
For years there's been a notion that spatial transcriptomics should allow for the definition of "spatial regions" or "tissue domains". In quotes because they're typically defined as "whatever the algorithm outputs". E.g. GASTON "spatial domains" vs. BANKSY "tissue domains". 2/
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It's easy to go in circles. Should cell types be distinguished on the basis of spatial data? Or are cell types purely transcriptomic notions without regard to space? Do spatial regions depend on cell types? Or should they be identified together? We went in circles for a while. 3/ Image
Read 19 tweets
Lior Pachter Profile picture
Jul 2
Aristotle was the first to notice honeybees dancing. In 1927 Karl von Frisch decoded the waggle. How it works was "explained" by MV Srinivasan AM FRS in the 1990s. Except @NeuroLuebbert found his papers are junk. A 🧵 about her discovery & our report: 1/arxiv.org/abs/2405.12998
First, if you're not familiar with the waggle, it's Nature magic! Watch this video for cool footage and an introduction.
Aristotle's observations in Historia animalium IX are arguably one of the first instances of observation driven inquiry and science. 2/
Karl von Frisch decoded the waggle, meaning he figured out how the number of waggles, and their direction, communicate information about the distance and direction of food sources. von Frisch won the Nobel Prize for his discovery. But exactly how it works remained a mystery. 3/ Image
Read 24 tweets
Lior Pachter Profile picture
Jun 27
A lot of bioinformatics requires editing sequencing reads to facilitate QC and make them suitable for processing. To help with such tasks, @DelaneyKSull developed splitcode, now published at 1/ academic.oup.com/bioinformatics…
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The input to splitcode are reads in FASTQ, along with a config file. The output can include edited reads or extracted subsequences, in FASTQ (including gzipped), BAM, or interleaved sequences to stdout. Regions can be identified using absolute location or relative anchors. 2/ Image
The splitcode toolkit was motivated by our need for a versatile tool that can perform a range of tasks from adapter trimming to barcode extraction. Specialized tools exist for many tasks, e.g. fastp, UMI-tools,, etc. Splitcode is more general enabling a lot with one tool. 3/
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Read 12 tweets
Lior Pachter Profile picture
May 6
For the second day of the week of observance of the Days of Remembrance of the Victims of the Holocaust a 🧵 about Sosúa.

Sosúa is a small beach town in the Dominican Republic that was founded by Jews fleeing Nazis in Europe in 1940. 1/
Sosúa is a beautiful place in Puerto Plata on the north coast of the Dominican Republic. About 56,000 people live there now.

But Dominican Republic? How did Jews end up founding a beach town in the Dominican Republic? How many Jews?

2/ Image
In 1938 a conference was held in Évian, France to discuss what to do about Jewish & Austrian refugees trying to flee persecution by the Nazis.

This is the same Évian of evian water. The company was founded in 1859 and was selling bottled water by 1908. But I digress.. 3/ Image
Read 9 tweets
Lior Pachter Profile picture
Apr 14
It's been great to see the positive response of @satijalab & @fabian_theis to our preprint on Seurat & Scanpy, and their commitment to work to improve transparency of their tools. One immediate benefit will be better practice of PCA in genomics. 1/🧵biorxiv.org/content/10.110…
PCA became a mainstay in genomics after the papers of @soumya_boston, Josh Stuart & @Rbaltman () and @OrlyAlter () ca. 2000 demonstrated its power for studying gene expression. 2/worldscientific.com/doi/abs/10.114…
pnas.org/doi/10.1073/pn…
Back then, having linear algebra on one's side was essential. A rich lab at that time might have something like a Sun Blade workstation clocking ~500MhZ w/ 2Gb RAM. So having fast SVD algorithms made PCA practical, when other methods based on more sophisticated models weren't. 3/ Image
Read 19 tweets
Lior Pachter Profile picture
Apr 7
The difference in @10xGenomics' Cell Ranger's default between version 6 and 7 is discussed in this thread, but it's such a big deal that it's worth its own thread.

tl;dr: in v7 Cell Ranger changed how it produces the gene count matrix leading to a huge difference in results. 1/
The change was described in release notes on May 17, 2022, which via two clicks lead to a technical note with more detail: 2/ cdn.10xgenomics.com/image/upload/v…
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To understand this technical note it is helpful to be familiar with the three types of reads that are produced in single-cell RNA-seq: spliced (M as a proxy for mature mRNAs), unspliced (N as a proxy for nascent RNAs), and ambiguous between both (labeled A). 3/ Image
Read 15 tweets

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