Question: I used Single Cell Gene Expression 3' LT (Low Throughput) v3.1 chemistry to prepare my sample. However, after running the data analysis, the chemistry shown in the web summary is 'Single Cell 3' v3' (not the expected 'Single Cell 3' v3 LT'). How does this affect the results I got?
Answer: If the 3' v3.1 LT library was analyzed as standard 3' v3 chemistry, the number of cells detected will likely be lower than using the correct chemistry.
In the example below, the results on the left were correctly detected as LT chemistry.
On the right, we forced the pipeline to use the wrong chemistry (standard 3'v3), and the number of cells detected is lower than expected. This is due to the minor updates in the cell calling algorithm for LT chemistry.
Therefore, we recommend using the default setting (chemistry auto-detection) and Cell Ranger 6.0 or later to analyze LT data.
If auto-detection fails (should be rare), you can specify chemistry as SC3Pv3LT for LT libraries.
Related article: Does 3’ LT (Low-Throughput) v3.1 chemistry use a separate barcode whitelist?