Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?

[edceeyuchen]

My files are below: Ab_C0042-25CN_S0_L001_I1_001.fastq.gz Ab_C0042-25CN_S0_L001_R1_001.fastq.gz Ab_C0042-25CN_S0_L001_R2_001.fastq.gz GEX_C0042-25CN_S0_L001_I1_001.fastq.gz GEX-C0042-25CN_S0_L001_R1_001.fastq.gz GEX-C0042-25CN_S0_L001_R2_001.fastq.gz

[luostrowski]

Were you able to figure this out?

[Hoohm]

Hello, CITE-seq-Count only runs on antibody fastq files, you need to merge them back using the cell barcode later after preprocessing.

Hope this helps.