How to split hashtag fastq?

How to split hashtag fastq?

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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,


single-cell


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