Great job @jeffvierstra.bsky.social ! Could you recommend a list of QC metrics to check for scATAC-seq datasets, with examples of good and bad quality? and do you have examples of papers that did a great job with the QC? thanks in advance :)

RAAAAAAHHH!!

... which may impact downstream analysis such as GRN modeling.

Thank you so much for putting this together! This will help us design our next experiments. I'd be very curious to see how GEM-X compares to Flex head-to-head. I foresee that Flex will better detect lowly expressed genes (such as TF),...

There is a huge difference between biochemically defined motifs and real life chromatin sites. In our 2016 paper we found all sorts of TFBS variants that would have never showed up in any database www.sciencedirect.com/science/arti...

Totally agree, but in practical terms that's what's gonna drive change

Of course, the main push back against this is: "if I publish my data I'll get scooped". And I totally sympathize with that, especially when people's careers are on the line. So we need to think as a community of ways of tackling this

Agreed! Not only that, pushing yourself to share code and data with the preprint ensures that it's properly done and not as an after thought or because "reviewers forced me too". What the latter accomplishes is GitHub repos that are impossible to navigate and data that is improperly annotated

Felicitats Pau!! Molt bona feina!!