Single-cell genomics assays are rooted in a handful of of technologies. They require physical isolation of cellular material, molecular barcoding, and library generation. Molecular modes include RNA, DNA (ATAC), protein and more which makes preprocessing challenging. 1/🧵 One challenge of data (pre)processing (distinct from processing) is that multiple data types that must be processed in a manner that minimizes batch effects. The challenge is ensuring that reads generated from assays are consistently catalogued, error-corrected, and counted. 2/🧵

In a new preprint, @lioscro, @JaseGehring, @lpachter and I describe a method and software (kITE) for quantifying orthogonal barcodes from assays such as Perturb-seq, Clicktagging, TAPSeq, CiteSeq, Multiseq, and 10xFeature Barcoding: 1/ biorxiv.org/content/10.110… Orthogonal barcoding has become a method of choice for multimodal single cell genomics. For example, multiplexing assays such as Clicktagging rely directly on click chemistry 2/

https://twitter.com/CarolynBertozzi/status/1578118227187552257

Using dimensional analysis I estimate that the energy contained in the awful #Beirut explosion was approximately 12 Terajoules = 3 kilotons of TNT. For reference the "Little Boy" dropped on #Hiroshima was ~13-18 kilotons of TNT. #orderofmagnitudephysics To estimate this, I used the following relationship between the energy of the explosion (E), the radius of the explosion (R), the time since explosion (t), and the density of air (rho).

1/6 Two days ago @NebulaGenomics announced the $299 genome in partnership with @TheBgiGroup. I was curious about the history of this cost so I looked historical price points curated by @genome_gov. Here are some results: @NebulaGenomics @TheBgiGroup @genome_gov 2/6 While the initial funding to create the first draft of the human genome was $2.7 billion, the actual price to sequence the final draft of the human genome was closer to ~100 million. This point is commonly missed. See here genome.gov/about-genomics…

1/ Worried to present @GoogleColab Python tutorials & R vignettes for complete #scRNAseq. Thanks to @satijalab @fabian_theis, @pmelsted, @lpachter @LambdaMoses @lioscro et al. and
biorxiv.org/content/10.110…
nature.com/articles/nbt.4…
genomebiology.biomedcentral.com/articles/10.11…
See
kallistobus.tools/tutorials @GoogleColab @satijalab @fabian_theis @pmelsted @lpachter @LambdaMoses @lioscro 2/ We've tried hard to make sure that the Python tutorials == R vignettes, so that language choice does not affect method. But we have not been able to get exact replicability.