CITE-seq-Count
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Hoohm
A tool that allows to get UMI counts from a single cell protein assay
Hi, sorry for asking again, but after going through the previous answers I have not found the answer that solves my problem. I have data that contains: HTOs, ADTs, 5'...
- [x] Rewrite data chunking - [x] Rewrite loading of CSVs with polars - [x] Rewrite Mapping in polars - [x] Rewrite barcode correction in polars - [x] Rewrite UMI...
I have a complex whitelist, as my scRNA-seq pooled samples were generated using the BD Rhapsody system. Essentially it has a CB region from 0-8, 21-29, 43-51 and UMI position...
Hi, I used to be able to use CITE-seq-Count 1.3 just fine, but I have tried to plug in results from a new experiment using python 3.7 and 3.8 and...
Hi, thanks for devoloping this tool! I'm trying to run citecount with 10xGenomics 5kPBMC public data as a test for the tool. in principle, it should work as i have...
Hi, I was wondering if you could help me with the following urgent issue: our protein lane has 34k cells (after mapping with CITE-seq-Count using -cells option, no whitelist), RNA...
Hi, I'm getting a different output each time CITE-seq count is run. My whitelist and parameters do not each each time. Is this expected? Is there anyway to control this...
Hi, thanks so much for developing this great tool. I just run a 10x Genomics scRNA sequencing on a pool of hashtag multiplexed sample. I tried to use the cmd...
Hi, Thanks for developing this great tool. I just have 2 questions regarding CITE-seq-Count. Question1: So, I have a multimodal scRNAseq dataset in which both CITEseq and Hashtag antibodies were...
I'm having issue running CITE-seq-Count because it's taking up too much memory. I tried running it on a cluster and even that got timed out. Start Time = 12/06/2021 23:26:26.956...
