bedapub / bedapub/besca

Documentation for citeseq workflow missing

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#161 4 comments 0 reactions 1 assignee Claimed by @schmucr1 View on GitHub
documentation enhancement
Dominant language
Python
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1d 4h
Merged PRs (30d)
3

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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