Comments (3)
I should probably mention that my version is conda installed (https://anaconda.org/bioconda/cite-seq-count) so v1.4.4 I think it is. The python version is 3.7.12 (as installed by mamba/conda)
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And there are 64k tags in that -t file...which I am starting to think is the essential issue here.
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Hello @dagarfield,
I'm guessing this would be too heavy. Have you tried to run it without cell barcode and UMI correction?
This software was not built for big datasets like this one I'm afraid.
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Related Issues (20)
- Percentage unmapped: 100 HOT 18
- Complex whitelist HOT 2
- Different "UMIs corrected" results between v1.4.3 and v1.4.5 HOT 2
- Code for running multiple lanes
- ValueError: columns cannot be a set HOT 5
- Python error when there are too many cells? Script never finishes HOT 2
- Cell Hashing on Multiome samples HOT 11
- bug in preprocessing.py -> get_read_paths() (version 1.4.3) HOT 1
- method keeps looking for whitelist when not provided. HOT 8
- 100% unmapped
- Include path to tag file in run report HOT 1
- barcodes with 0s in all protein tags and unmapped roll HOT 2
- Running Cite-Seq-count with next GEM protocol HOT 2
- Pandas error after correcting UMIs HOT 1
- Allow to split fastq or get list of readID per cell HOT 2
- Unable to locate temp file while merging results
- Does not compile using Python version > 3.9.x please fix.
- Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?
- Please, trim all sequences at the same length.
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