carbycrab

> (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...

Thank you for your reply. 1. I've attached `tags.csv` here. [tags.csv](https://github.com/Hoohm/CITE-seq-Count/files/7455025/tags.csv) 2. I tried re-running the command (this time including: `--whitelist 3M-february-2018.txt` and `--start-trim 10`) on merged fastq files and...

I tried running the command without `--white-list` on just the first 10000 reads and this what I get: `run_report.yaml`: ``` Date: 2021-11-03 Running time: 5.645 seconds CITE-seq-Count Version: 1.4.3 Reads...

@Hoohm Thanks for that suggestion. I tried with a merged R1/R2 files and separate R1/R2 files, both specifying trim 9, but still got 100% unmapped

Hi, I am also having the same problem. Any solutions yet?