Hi all, does anyone have experience running a Nextflow scRNA-seq pipeline with BD Rhapsody single-cell data?

Hey, the pipeline is basically a wrapper around multiple aligners. It allows quite flexible configuration of the aligners, so you can make it fit your needs. So I am not exactly sure how to handle BD Rhapsody data, but if you know how to configure any of the available aligners to handle this data, I can probably show you how to make this work with the pipeline

hi @Nico Trummer thank you for your response. I looked into the available aligner options, but Cell Ranger is still focused on 10x Genomics, so it doesn’t support BD Rhapsody directly. I also tried running an open-source Nextflow pipeline for BD data, but I ended up running out of RAM before it could complete. Given the options in this pipeline — maybe UniverSC will work.

Maybe this is useful for you? Apparently, it internally uses STAR (which might allow you to use #CE8SSJV3N), but an LLM told me it would also work with STARsolo with a configuration as below:

STAR --runThreadN 16 \
     --genomeDir /path/to/genome_index \
     --readFilesIn Read2_cDNA.fq.gz Read1_Barcode.fq.gz \
     --soloType CB_UMI_Simple \
     --soloCBwhitelist /path/to/combined_whitelist.txt \
     --soloCBstart 1 1 1 \
     --soloCBlen 9 9 9 \
     --soloUMIstart 52 \
     --soloUMIlen 8

If you can confirm this works with STARsolo, I could adapt #CHN5BV5DW to support this natively