I have been searching for a cell barcode (CB) whitelist for Drop-seq, but it seems difficult to find a standard list. On the other hand, it is relatively easy to find whitelists for 10x protocols.
If no whitelist is available, what would be the best procedure here? I have used STARsolo to align the reads so far, and it accepts a parameter configuration of
--soloCBwhitelist None if no whitelist is available. For all intents and purposes, I presume that I can then just assume that the cell barcodes that STARsolo identifies from one sample is a whitelist that I can use across all samples?
I presume that other programs, e.g., UMI-tools and Alevin, can also take a FASTQ pair and be used here?
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