jon-xu

试试看这个？http://www.chamiji.com/chinarank

Hi Marcus, The contents are: ['all_mod_bases', 'u_mod_llrs', 'u_can_llrs']

So the error log of the batch file looks like this: (base) [uqjxu8@wiener vac]$ cat logs/megalodon_calibrate_error.txt [20:33:16] Parsing log-likelihood ratios [20:33:21] Computing u modified base calibration. [20:33:21] Computing reference emperical...

Just attached the two result files here: https://cloudstor.aarnet.edu.au/plus/s/KHg7s6wsU0aGjU0 [calibrated.pdf](https://github.com/nanoporetech/megalodon/files/9136254/calibrated.pdf)

Hi Marcus, did you have a chance looking into the attached result files, please?

You can plot the pseudotime(cds) against the clusters(cds), which can show you which cluster is earlier which is later. But I also don't get it why we need the numbers...

Same question here. We tried running velocyto on both cellranger outputs (default setting and include-introns setting). Here are what we observed: 1. cellranger with include-introns has more (about 5%) valid...

I have the same question, I appreciate that velocyto can work on snRNA based on another issue, but shall we use the output from Cellranger by setting "include-introns" flag or...

Thanks Marcus, I'll double check the read positions and let you know.

waiting for admin to install the latest gcc on HPC...