Patrick Roelli

@seb-mueller Realy nice modifications! I like them :) Found a couple of mistakes here and there. I'm having some issues pushing to remote for some reason. Probably linked to my...

Hello @dylkot When umi_tools was added for the whitelist, I got better results (more reads) than the standard drop_seq tools and by combining both we should get the best of...

From your plot I would consider the selection to be ok. As we don't see a clear knee/bend, I would rather stay conservative. I would look at the violin plots...

Hello @caramirezal I would not use relative paths at all. We sometimes get odd behaviors with those. There is a test data in the .test folder. You can download this...

Hello, I have the same problem. I tried to install and run from source but I got into issues with the dbconnect not working properly. Bad syntax fo the sql...

Hello Alana. The only way that would fit here today is my rewriting R1 and putting all the cell barcodes positions first and then umis last. Then run with the...

Hey @brindavjk that wouldn't be what you're looking for. The saturation rate is answering how many more molecules (UMI) do I get if I sequence deeper. You should calculate total_umis/total_reads*100...

Happy to see fellow users help each other. @dianitasusilo maybe a sliding window approach might help yes: `--sliding-window` is the option you are looking for. @sopenaml Could you check out...

The cell barcodes that should be in R1, just before the UMI On Wed, 13 Apr 2022, 11:46 sopenaml, ***@***.***> wrote: > Hi Patrick, I'm not sure which barcodes you...

Hey @sopenaml, I need to rephrase what I mentioned earlier. Depending on what chemistry kit you used, it's possible that your R1 barcodes(cell barcodes) linked to one library (GEX, VDJ,...