Unclear Usage for CITE-seq Data

[DarioS]

I would like to see instructions for analysing CITE-seq data. For example, my data looks like

$ ls *
CITE:
BH_pool1_S1_L001_I1_001.fastq.gz  BH_pool1_S1_L002_R1_001.fastq.gz  BH_pool1_S1_L003_R2_001.fastq.gz
BH_pool1_S1_L001_R1_001.fastq.gz  BH_pool1_S1_L002_R2_001.fastq.gz  BH_pool1_S1_L004_I1_001.fastq.gz
BH_pool1_S1_L001_R2_001.fastq.gz  BH_pool1_S1_L003_I1_001.fastq.gz  BH_pool1_S1_L004_R1_001.fastq.gz
BH_pool1_S1_L002_I1_001.fastq.gz  BH_pool1_S1_L003_R1_001.fastq.gz  BH_pool1_S1_L004_R2_001.fastq.gz
GE3:
BH_pool1_S1_L001_I1_001.fastq.gz  BH_pool1_S1_L002_R1_001.fastq.gz  BH_pool1_S1_L004_I1_001.fastq.gz
BH_pool1_S1_L001_I2_001.fastq.gz  BH_pool1_S1_L002_R2_001.fastq.gz  BH_pool1_S1_L004_I2_001.fastq.gz
BH_pool1_S1_L001_R1_001.fastq.gz  BH_pool1_S1_L003_I1_001.fastq.gz  BH_pool1_S1_L004_R1_001.fastq.gz
BH_pool1_S1_L001_R2_001.fastq.gz  BH_pool1_S1_L003_I2_001.fastq.gz  BH_pool1_S1_L004_R2_001.fastq.gz
BH_pool1_S1_L002_I1_001.fastq.gz  BH_pool1_S1_L003_R1_001.fastq.gz
BH_pool1_S1_L002_I2_001.fastq.gz  BH_pool1_S1_L003_R2_001.fastq.gz

I wonder if Vireo can only process the GE3 folder and I need to write my own preprocessing for the CITE folder (matching cells).