We have hashtag scRNA-Seq data (fastq1, fastq2, HTO-fastq1, and HTO-fastq2) each including 6 samples. We know that there are ways to calculate counts for each UMI for each sample (scRNA-seq CITE-seq-count bioinformatics). However, we would like to split the fastq files by the sample. Could you please let me know if there's a tool or a way to modify existing tools (e.g., CITE-Seq-cnt mentioned above) for that purpose?

Thanks,