CITE-seq-Count
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Hoohm
A tool that allows to get UMI counts from a single cell protein assay
Hello, Thank you for developing such an innovative package! I've been trying to run `CITE-seq-Count` on my 10X V3 data, but keep on getting 100% unmapped returned. This is the...
We are trying to demultiplex our samples using Cite-seq but we are getting low overlap between cell barcodes and hashtag barcodes. We used the same pipeline on our previous experiment...
``` import yaml with open(os.path.join(path_data, "report/run_report.yaml"), "rt") as fin: report = yaml.load(fin, Loader=yaml.FullLoader) ``` I'm getting this error: ``` while scanning for the next token found character '\t' that cannot...
Hi, I am starting with CITE_seq-Count and its output. The Tool looks amazing. After running the script I got an output that is very populated by unmapped TAGs. I can...
Hello, Thanks for making this tool. I have a quick question about the parameters involving cells. User can input the number of cells expected in the run, and/or also input...
Hi, I wanted to confirm that we are calculating the saturation rate correctly for our CITE-seq data. We have a run_report.yaml output as follows: Date: 2020-10-29 Running time: 4.0 hours,...
Hi, Thank you for developing such a convenient program, CITE-seq-Count, which helped our lab a lot, so far. But recently when I processed the fastq data (total 516,131,880 reads of...
Currently trying to run a very large ADT library (~500M reads) for a CITE-Seq project. First, I tried running on all 500M reads at once, with 8 cores. I got...
Hey, first of all thank you so much for the incredibly useful and well documented CITE-seq-count tool. I was going through the documentation and also tried to figure out from...
Hi, I have 2 issues, one is when setting the estimated cell number, CITE-seq-Count appears to force the cell count to that number. I am worried this can lead to...
