Comments (2)
Hoohm
commented on July 26, 2024
Hello @rosaxma.
If I recall properly, this is mostly linked to a bug that was miscounting some single or two umis correction. The code counted them as corrections but didn't actually correct any UMIs.
More relevant to your question would be to compare the umi count output. This would be more accurate in terms of consistency.
I would guess that the count matrix should be the same. The number shown in the report of 1.4.3 is probably overinflated and the 1.4.5 is properly reporting the number of UMIs corrected.
A scatter plot with a correlation value should give you what you expect.
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rosaxma
commented on July 26, 2024
Thank you!
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Related Issues (20)
- 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
- Discussion question -- is it normal to take so long? HOT 3
- 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.
- CITE-seq-Count run gets stuck
- ValueError: columns cannot be a set HOT 3
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