Patrick Roelli

I would propose the use of cutadapt: https://cutadapt.readthedocs.io/en/stable/guide.html?highlight=adapters#multiple-adapters Seems it would support this by providing the constant regions as adapters. awk and sed custom bash script would also work pretty...

This issue should be fixed with version 1.4.4 Which version are you running? Maybe just give it a couple more hours. On Mon, 8 Feb 2021, 03:22 YingzhengXu, wrote: >...

Hello @jamesboot A few things I would test out. I think it might be because this version doesn't check for 0 counts and I think this is what is happening...

I think this is a bug with the newest pandas version: https://github.com/facebook/Ax/issues/1153 Can you try to reinstall with pandas 1.4?

If you run with ellipse = FALSE it will run fine. The issue is that you probably don't have enough samples per group to actually make the ellipses. ``` g

Hello @yeroslaviz, you will need to run both R1 and R2 files as they are both necessary to run the command. Have you had a look at the [documentation](https://hoohm.github.io/CITE-seq-Count/Running-the-script/)? It...

Having the same issue with a dropseq pipeline.

I'm using dropseq data from the McCarroll pipeline and getting the same problem. Haven't been able to figure out why either :(

Hello @dagarfield, I'm guessing this would be too heavy. Have you tried to run it without cell barcode and UMI correction? This software was not built for big datasets like...

Hello @bassanio did you already go through the [documentation](https://hoohm.github.io/CITE-seq-Count/Running-the-script/)? If so, could you maybe tell me specifically what you need help with?