It’s not totally up to date but still may be useful: fiberseq.github.io/index.html

@mollyschumer.bsky.social if the data is pre SPQR chemistry I would recommend fibertools. If it’s new data then you can use Jasmine from Pacbio, Andrew and I spent a fair amount of time looking at the Jasmine results and they look good. And it will all still work with downstream fibertools commands

🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020.

It's a very cool method for adding chromatin accessibility data to native LRS experiments.

You should definitely check out the original paper: www.science.org/doi/10.1126/...

Had the privilege to also see the magnificent session S10 - on the non-coding genome.
Again top-notch science with great presentations and style of bring complex matters to a broad audience! What a treat!
Thanks @mrvollger.bsky.social; @elfridedebaere.bsky.social and Musa Mhlanga @eshg.bsky.social

So who carried it? Hope you didn’t enlist Phil lol

Alfred is the answer! (imo) www.alfredapp.com

I do fear with the DAG that the filesystem is the rate limiting factor but I have never benchmarked it. I know executing the same pipeline in a totally empty directory can be much faster though.

I have felt the DAG pain, haven’t had issues on the slurm side but did have grid issues for years. I think the executor plugins while it has been buggy is a step in making distribution better.

I think Johannes has talked a few times about wanting to use rust for the DAG, I know I would want that.