Cas-Analyzer after Barcode Splitter

Hi all,

I used Barcode Splitter to test separate my paired-end Fastq file, and I have unique barcodes on both 5’- and 3’- ends.

I found that for a barcode pair, for example, BC-Forword1, I have 50000 sequence reads in total.
In its reverse, BC-Reverse1, I also have 50000 reads.

What when I analyze these these files with Cas Analyzer or PE-Analyzer, the total reads it takes into calculation is only ardound half, like 20000 reads, but not 50000 reads.

Anyone know what’s wrong with my operation?