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May 19 • 25 tweets • 10 min read
Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from @ensembl et al., @NeuroLuebbert developed gget:
biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget).
gget has many uses; a 🧵on the its amazing versatility: 1/
gget works from the command line or python. Just `pip install gget`.

Need reference files for your analysis? 2/
Simple with `gget ref`...3/
Gene ID conversions *used* to be a pain... 4/
... with gget... not anymore! 5/
Here's a common task that anyone who has done #RNAseq or #scRNAseq has faced: 6/
The solution is now one line: 7/
This tasks requires a lot of clicks on the @GenomeBrowser... 8/
gget.seq returns the canonical sequence unless you ask for all isoforms: 9/
You don't need to take a class to BLAST with gget: 10/
BTW gget can also take FASTA files as input. 11/
And no more need to choose sides in BLAT vs. BLAST twitter wars... 12/
Just run both! 13/
We found in our work that aligning genes and/or isoforms can be useful in the course of #scRNAseq analyses. So we built an alignment interface. 14/
No problem aligning the colored blocks 🙂 15/
This is an excellent question... 16/
gget provides a solution via a convenient interface to @alexlachmann, @AviMaayan et al.'s ARCHS4. 17/
Hopefully gget also helps in training / classes / workshops. 18/
Now... every PI wants a GO enrichment analysis. 19/
We got that covered (thanks to Enrichr from @MaayanLab). 20/
Putting it all together, gget can, in a few lines, easily take care of more complicated tasks such as this one... 21/
... just 5 calls to gget!

The ability to do free-form searching is, we think, going to be particularly useful. 22/
We'd appreciate any feedback via Github, including requests for additional features: github.com/pachterlab/gget 23/
Finally, gget was written entirely by @NeuroLuebbert, but thanks to @agalvezmerchan, @kreldjarn, Matteo Guareschi, @sinabooeshaghi, and @lioscro for helpful feedback and advice on the tool. 24/25
Special thanks to Dash Coffee Bar for facilitating deep contemplation of the RNA-seq smoothie metaphor...

25/25

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More from @lpachter

Lior Pachter Profile picture
May 11
The analysis of single-cell RNA-seq data begins with "normalizing" counts. In a preprint with @sinabooeshaghi, @IngileifBryndis & @agalvezmerchan, we examine the assumptions and challenges of normalization, benchmark methods, and motivate solutions: biorxiv.org/content/10.110… 🧵 1/
We weren't particularly interested in studying normalization, but faced a vexing problem related to normalizing feature barcodes. In scouring the literature for solutions to our problem, we became increasingly confused rather than enlightened about how to normalize our data. 2/
We started with the excellent recent review / expository article by @const_ae & @wolfgangkhuber that looks at strengths & weaknesses of many methods: biorxiv.org/content/10.110…. It became clear to us that a central question is how to normalize depth w/ gene count overdispersion. 3/
Read 25 tweets
Lior Pachter Profile picture
Mar 22
"..antibody-based and lipid-based methods are simple, straightforward and generally applicable to a wide range of single cell applications and platforms, while genetic cell labeling and chemical labeling with oligonucleotides can be more challenging." Huh? genomebiology.biomedcentral.com/articles/10.11…
We have found the exact opposite to be true. nature.com/articles/s4158…
Tagging with chemical oligos does not require design of antibodies to specific proteins. Hence it is essentially universal with respect to organism, which is why it can be used to multiplex, say, jellyfish. science.org/doi/10.1126/sc…
Read 4 tweets
Lior Pachter Profile picture
Mar 17
When I went on the job market for my first job after I had been a postdoc I applied to only 3 schools where I really wanted to go (why waste people's time?). I got only one job (@UCBerkeley). 1/
I obviously had no other offers, but someone else in my field (computational biology) who applied to a different department did. The chair of my department wrote to the dean and explained that it would be fair to start both of us at the same salary. 2/
The dean wrote back and declined, explaining that "while I agree with you that it would be the right thing to do, in the absence of an outside offer [for Lior] I cannot approve a salary beyond the minimum." I still have the letter. 3/
Read 6 tweets
Lior Pachter Profile picture
Mar 9
This #covid19 chart from Iceland shows the data from a small country in the North Atlantic, but it tells the story of #covid19 worldwide.🧵1/
Mitigation procedures / lockdowns don't work? Why yes... they do! 2/
Indoor parties before and during Christmas without vaccination or masks aren't a problem? Well yes... they are! 3/
Read 7 tweets
Lior Pachter Profile picture
Mar 7
I recently saw a moving performance of Elgar's cello concerto by @CamilleThomasOF with @PBortolameolli conducting the @LAPhil. I've probably listened to this piece thousands of times and know all the famous recordings, but I'd never heard it live. @CamilleThomasOF was incredible. Image
She will obviously draw comparisons to Jacqueline du Pré, but comparing a live performance to a recording is a fool's errand. What I can say that I heard in @CamilleThomasOF's performance tones, sounds, and ideas that I never knew were in the piece.
Elgar's cello concerto was written shortly after World War I, and @CamilleThomasOF's performance against a backdrop of violence that echoes some of the tragedies not only of the Second World War, but also of the Great War, was profound.
Read 5 tweets
Lior Pachter Profile picture
Mar 7
I recently saw a lecture by Eric Lander in which he talks about the history of comparative genomics, puts up a slide with pictures of 23 animals (monkeys, a dog, a horse etc.) + one black baby, and then refers to them all as "cute animals" 😱. 1/6
Trying to afford the speaker the benefit of doubt... I figured perhaps he misspoke and meant that the animal genomes were intended to better understand the human. But the history of genomics is whites only. Even in 2009, 96% of GWAS had been on whites. sciencedirect.com/science/articl… 2/6
So why pretend genomics prioritized black kids, when the reality in 2017 was that "Individuals with African ancestry [were] not receiving the same level of care as individuals of European ancestry due to limitations in available data"? link.springer.com/article/10.100… 3/6
Read 6 tweets

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