CITE-seq-Count
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Hoohm
A tool that allows to get UMI counts from a single cell protein assay
I have a very deeply sequenced barcodes library and I expect a substantial amount of UMIs to not be real. We expect those "fake" UMIs to have very low read...
Hi @Hoohm, I have been trying to align some ADT data and the process pool keeps crashing after maxing out the RAM available on the system. I am running on...
Hello, I have been trying to use the CITE-seq-Count script, but cannot get it to complete. It keeps getting hung up at the "Looking for a Whitelist" process. Any ideas...
Hello, We are exploring QC tools that require the full count matrix (including background) for the purpose of quantifying barcode levels from ambient drops. These expect the cell ranger unfiltered...
Hi, I ran cite-seq count on cell hashing data using the whitelist from the cellranger filtered output. Since it's 10X V3 data, I mapped the cellranger filtered output barcodes to...
Hi @Hoohm , Thank you again for the easy to use package! Just a suggested enhancement feature that i think a lot of people might be interested in. Would be...
Our objective is to test TCR Ab Oligos to define starting cell type, and also to Test the ability to pool samples with TCR Ab Oligos. We are using 10X...
The document says the default value is 3, but it seems that the tool actually uses `--max-error=2` by default. https://hoohm.github.io/CITE-seq-Count/Running-the-script/#optional
Hello, umi tools 1.0.1 was already released in December https://github.com/CGATOxford/UMI-tools/releases With a normal fresh install of everything you get: Traceback (most recent call last): File "/opt/conda/envs/bio/bin/CITE-seq-Count", line 5, in from...
hi all, trying to run citeseq count using 10x data but got this error following my command: CITE-seq-Count -R1 R1_001.fastq.gz -R2 R2_001.fastq.gz -t tag_list_GEM1.csv -cbf 1 -cbl 16 -umif 17...
