Documentation for citeseq workflow missing
- Dominant language
- Python
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Description
Add here important/cautious notes:
- Use an Antibody name different to the gene name. `merge_mtx` and `besca` will not raise error/warning but, when reading the matrix with citeseq=true, it will make the index (e.g SYMBOL) unique by appending a number string to each duplicate index element: ‘1’, ‘2’, etc.
e.g if in genes.tsv you have:
```
1 CD4 Antibody Capture
ENSG00000010610 CD4 Gene Expression
```
Then CD4 (for gene expression) will be converted to CD4.1. Important to consider this name change when ploting CD4 gene expression (otherwise can seem not expressed).
Suggestion: raise a warning in besca if there are duplicated names and indicate the name changes. (would not raise an error because the duplicated names come from the input 'feature_ref.csv' file before running cellranger)
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