Hi #CHN5BV5DW I am currently working with a 10x Genomics Multiome dataset containing both snRNA-Seq and scATAC-seq data. I would appreciate any guidance on the following: Can I use existing pipeline (https://nf-co.re/scrnaseq/4.1.0) for pre-processing and aligning GEX and ATAC fastq files?

In short, yes, if I not misunderstand your question, the scrnaseq webpage already have some guidelines to run it via cellranger multi aligner