But in reality, each sample might have multiple fastq files, like: simpleaf quant --reads1 L1_R1.fq,L2_R1.fq,L3_R1.fq \ --reads2 L1_R2.fq,L2_R2.fq,L3_R2.fq

4/ Another example: Single-cell RNAseq quantification with simpleaf For one sample: simpleaf quant --reads1 sample_R1.fq --reads2 sample_R2.fq

@ZeroDotCMD im having issues with the dxc extruder runout while using simpleaf. Any idea how i could.solve this?

Yes factory reset, and use simpleaf You can use the helper script. Factory reset option that does the quick reset that retains root access after to make life easier Then move to simple af after

Well im going to update the eddy atm but im getting conflicting info on wether to use simpleaf or helper script (currently using helper) and if i should factory reset the machine again.

I have a Creality K1C with "SimpleAF" (klipper) firmware and it's been great so far. I block it's internet access at the firewall. It's certainly not as user friendly as stock software, but it's worth it to me.

10x Flex Gene expression support is now part of the piscem -> alevin-fry workflow, and also has a nice, low-friction command in simpleaf! Check out the tutorial here (combine-lab.github.io/alevin…). This was a major feature upgrade, so we're looking for testers and feedback :).

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Prusa - top choice but more expensive. Best for supporting open source hardware software, and a potentially more ethical hardware pipeline Snapmaker U1 - best up and coming multiple color tools. Bambu Lab is good if you're fine with a more closed ecosystem and mandatory cloud. I suppose you can do dev lan mode only on them. The most plug and play option if you're more concerned about the results than the process. K1 Max is fine with a few updates: requires cartographer simpleaf firmware imho. You might not be familiar with this toolset but you essentially just control it from your browser.

I'll regret claiming success too soon, but the @Cartographer3D probe SimpleAF klipper firmware is starting to make my K1's usable. If I could go back in time I wouldn't buy a K1, but it's what I have for now so I'm committed to getting it printing well. Getting it to this point has been a pain but so far I'm happy, though only a few prints in. Still want a new shroud, overhaul of the X rail, better chamber filtration, etc.

Cartographer simpleAFを使うべく輸入したMX1.25とかJST1.25とか呼ばれてる実はMolexのコネクタが届いたので使える様にケーブルの順番を変更した これから反対側のコネクタを圧着して完成させていきます

QCatch accepts the output directory of either alevin-fry or simpleaf as input and outputs both an HTML report and a richly-annotated H5AD object. This design choice enables seamless integration with the scVerse ecosystem.

The dumb guys are bad and the good guys are smart simpleAF

Things that come to mind: - detecting chem e.g. v2, v3, 5’, GEM-X - auto-selecting whitelist - maybe the biggest delta in usability is handling multiomics - CR typically handles ATAC / ADT / TCR files smoothly, while these are a little fiddly with simpleaf Hope that’s a start!

I still hope people choose to use open-source, transparent, and auditable methods. For example, we will be happy to add support to ensure that alevin-fry and simpleaf work well with this tech.

After some struggles with #bioconda (again), piscem 0.9.0 and simpleaf 0.17 are both available! The new piscem comes with some bug fixes, new features, and some convenience geometry flags. The new simpleaf propagates these flags and adds some other quality of life improvements!

Heads up! Rob Patro @nomad421, associate professor at UMD and key player in computational genomics, will speak at #scverse2024! His work on tools like salmon, alevin, and simpleaf is groundbreaking. Catch his insights on genomic algorithms! Register here: scverse.org/conference2024/r…

Processing single-cell RNAseq counts with simpleaf (alevin-fry) youtube.com/watch?v=Dh3pGBaJ…

¿Ahora qué hacer con los Banners? Tráelos a SimpleAF para que puedan transformarse en otros artículos y apoyas a mujeres trabajadoras que además tienen niños con discapacidad y esta forma de empleo les permite cuidar a sus familias.