AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Docs request: FAQ about gene id conversion

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#837 1 comment 0 reactions 0 assignees View on GitHub
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Description

### What is the documentation improvement or update you wish to see?

Many previous single-cell analyses use gene symbols as their primary identifiers, while we use the more stable Ensembl IDs. We should provide clear instructions on how to convert between identifiers. We should be sure to note that such conversions should be done before conversion to Seurat (if that conversion is required), and how to deal with duplicate gene symbols.

### Is there any additional context you would like to provide?

We provide the gene symbols within our SCE objects, but we do not do anything to deal with duplicate gene symbols. We should carefully investigate what conversion we want to recommend: do we take the values from the "first" gene id, the gene id with the highest expression, or perhaps sum expression across the duplicated set?

The proper investigation of this question might require looking at CellRanger default references (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz ) to determine which gene annotations were used there, which should allow us to make the best recommendations.

### If this request is for an existing documentation page, please provide the link here.

https://openscpca.readthedocs.io/en/latest/troubleshooting-faq/faq/

Contributor guide

Open the contributing guide

Research direction

Start with the existing troubleshooting FAQ page and inspect how SCE objects expose gene symbols. Investigate the linked CellRanger GRCh38 reference and compare the proposed approaches to duplicate gene symbols before documenting conversion timing relative to Seurat. Done means the FAQ explains identifier conversion, duplicate handling, and when to perform it.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics, documentation
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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