cpflueger2016

(1) Do you mind posting your `tag.csv` file? (2) Also, did you try to run `CITE-seq-Count` on just on a single fastq file (e.g. L001 only) or a merged fastq...

### UMI counts output ### Read counts output Hey @Hoohm, thank you so much for your reply and the detailed explanation. I was thinking that this what it meant but...

Hey @Hoohm, thanks for the followup. As you have pointed out, I do expect a much stronger amplification of tags in certain cells. These "barcodes" are driven by a promoter...

Sure thing. The tags (barcodes) are expressed in a cell after lentiviral transduction. They have a 5' PCR handle to attach the P7 handle by PCR and on the 3'...

Hey @Hoohm, I did a bit of deeper digging and found that the CITE-seq tool is working perfectly fine. The issue I'm seeing is related to late-stage PCR based barcode...

Hey @Hoohm, thanks heaps for your reply. Would love to have a chat with you. I just signed up for discord and my number is cpflueger#4139. Feel free to send...

Hey @Hoohm, I have given the `switch_mod` branch a go and saved the output to a text file. However, I do not see the output on the command line as...

Hey @Hoohm, I successfully updated the branch with your help and ran the CST from the switch_mod branch. But there seems to be an error: `Traceback (most recent call last):...

Hey @Hoohm, you're a legend mate! First off, I created a separate conda environment on our server with python3 installed. Then I had to install the branch on our server...

If you could keep the STDOUT output as a "debug" option that would be huge since it is really helpful to understand what is going on regarding cellbarcode/UMI swaps. And...