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Lior Pachter Profile picture
@lpachter
Feb 1, 2020 • 3 tweets • 5 min read • Read on X
In our #RNAseq & #scRNAseq work we use @ensembl's databases. Two months ago @sinabooeshaghi noticed some inconsistencies between @ensembl's cDNA fasta and GTF files and investigated with @lioscro. Now @LambdaMoses has written up an in-depth analysis: fromsystosys.netlify.com/2020/01/31/com…
@ensembl @sinabooeshaghi @lioscro @LambdaMoses To work around the inconsistencies, the `kb` wrapper for kallisto and bustools can easily generate genome consistent transcriptomes. pypi.org/project/kb-pyt…
@ensembl @sinabooeshaghi @lioscro @LambdaMoses We're not the only ones to stumble into this:
Would be great if @ensembl included the code used to make the various files distributed. Maybe they exist at github.com/Ensembl but couldn't find them. cc @PaulFlicek

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More from @lpachter

Lior Pachter Profile picture
Sep 10
So this plagiarism thing has happened to our lab.. again. This time it's plagiarism of our poseidon syringe pump paper @booeshaghi et al., 2019 in @SciReports:
Text has been plagiarized, as well as figures copied directly here: 1/🧵nature.com/articles/s4159…
ijirset.com/upload/2024/ma…
Here is figure 1 from our paper (LHS) and figure 1 in the plagiarized paper (RHS) published in the "International Journal of Innovative Research" 2/ ijirset.com/upload/2024/ma…

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The text seems to have been rewritten with an LLM. Our introduction (LHS) vs. the plagiarized version (RHS): 3/
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Read 11 tweets
Lior Pachter Profile picture
Aug 16
I've checked this paper out, as instructed. I was also interested in the main result for personal reasons: I'm 51 years old. Is it true that I've just gone through a major change? And that another one awaits me in just a few years?

Some comments on the paper in this thread 1/🧵
The main result about major changes in the mid 40s and 60s is shown in this plot (Fig. 4a). First, I redrew it with axes that start at 0, so the scale of change here was clearer. Not as impressive, but maybe it's a thing? 2/
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The authors say that this finding is even corroborated in another study (ref 14). But that's not true. I looked it up, and it shows something totally different (see RHS Fig 3c from ref 14). No change in mid 40s, but a change in the mid 30s, and the real change in the 80s 😕 3/
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Read 17 tweets
Lior Pachter Profile picture
Aug 10
I recently posted on @bound_to_love's work quantifying long-read RNA-seq. In response, a scientist acting in bad faith (Rob Patro @nomad421) trashed our work. This kind of mold in science's bathroom is extremely damaging so here's a bit of bleach. 1/🧵
At issue are benchmarking results we performed comparing our tool, lr-kallisto, to other programs including Patro's Oarfish. Shortly after we posted our preprint Patro started subtweeting our work, claiming we'd run an "appallingly wrong benchmark" and that we're "bullies". 2/
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This was followed, within days, by Patro posting a hastily written preprint disguised as research work on benchmarking, but really just misusing @biorxivpreprint to broadcast the lie that our work "... may be repeatable, but it appears neither replicable nor reproducible." 3/ Image
Read 25 tweets
Lior Pachter Profile picture
Aug 1
This recently published figure by @Sarah_E_Ancheta et al. is very disturbing and should lead to some deep introspection in the single-cell genomics community (I doubt it will).

It demonstrates complete disagreement among 5 widely used "RNA velocity" methods 1/ Image
This is of course no surprise. In "RNA velocity unraveled" by @GorinGennady et al. in @PLOSCompBiol we wrote 55 page paper explaining the many ways in which RNA velocity makes no sense. 2/ journals.plos.org/ploscompbiol/a…
We're not the only ones to understand how flawed RNA velocity is. The paper from the groups of @KasperDHansen and @loyalgoff is titled "pumping the brakes on RNA velocity". The whole notion of putting arrows on UMAPs is ridiculous. 3/genomebiology.biomedcentral.com/articles/10.11…
Read 6 tweets
Lior Pachter Profile picture
Jul 29
I was recently schooled on some Gen Z and Gen Alpha brainrot. Here's a yap about it:

1/🧵
Delulu:

"I just submitted my R01. I'm sure this one is going to finally get funded!"

You're delulu.

2/
Cap:

"Reviewer #3 accepted our paper without revisions no cap!!"

You're capping be for real! 3/
Read 13 tweets
Lior Pachter Profile picture
Jul 25
Challenge accepted. Here are a few comments on the paper after starting to wade through its massive content. The paper in question is 1/🧵 nature.com/articles/s4158…
First, the claim that "lower OPC fraction across regions and, in particular, in non-neocortex regions was significantly associated with impaired cognition (Supplementary Fig. 37d)" is not true. Supp. Fig. 37d is below. I've boxed in red the panel the claim is based on. 2/ Image
The R^2 value, i.e. proportion of variance explained is 0.0256. The "significance" claim is based on the reported p-value of 0.0071 which is less than 0.05. However significance vanishes once one corrects for the number of tests performed. 3/
Read 22 tweets

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