Question: Does Single Cell Gene Expression 3' LT (Low-Throughput) v3.1 chemistry have a separate barcode whitelist? Or it uses the same barcode whitelist as 3’ v3.1 chemistry?
Answer: A barcode whitelist is the list of all known barcode sequences that have been included in the assay kit and are available during library preparation.
Single Cell 3’ LT v3.1 chemistry has a separate barcode whitelist. You can find the LT barcode whitelist file (with "LT" in the file name) bundled inside your Cell Ranger installation:
Note that the whitelist for 3’v3 LT is only available starting from Cell Ranger version 6.0.