Hi everyone! Our group did an experiment which generated a bulk immunoseq and a 5' 10X Genomics GEX dataset (scRNAseq). We wonder if and how compatible the airrflow pipeline is with 5' 10X GEX data? Would it be possible to export the alignments in AIRR format? Cheers, AS

Hi @AnneSofie, the pipeline focuses on the analysis of 5'10X BCRseq or TCRseq data, it does not process the GEX data. If you’re interested in running it for the BCRseq or TCRseq data, you can start from the raw fastq reads (it will run Cellranger VDJ for you) or from the AIRR files that cellranger outputs (with the assembed mode). Here are the docs, let me know if something is unclear: https://nf-co.re/airrflow/4.1.0/docs/usage

@Gisela Gabernet I was afraid so, I was hoping for an alternative strategy to use my GEX data for this. Thank you for your reply!

Hi @AnneSofie, could you explain a bit better what you want to analyze? Do you want to extract BCR / TCR sequences from GEX data? Or analyze only the gene expression of the scRNAseq data? We also offer an option to extract BCR/TCR sequences from 5'GEX data with TRUST4