Low percentage of reads with consistent barcodes in Split-Seq run I am following this answer to select reads with allowed barcodes from a Split-Seq run. In particular, I have a whitelist for each round of barcodes (3 rounds) and I filter out reads which have more than 1 Hamming distance from allowed barcodes.

However, after filtering, the number of reads remaining are only the 0.7% of the original number of reads before filtering (169k from 22M). Is this normal, or what may be the underlying issue here?
In my case the problem was due a wrong set of allowed round1 barcodes, therefore the filtering pipeline was removing most part of the reads. In particular, with the right barcode1 whitelist the total number of reads after filtering is 17M (about 100 times more).