I just downloaded some single cell multiomics original sequencing data (.fastq.gz) from human cell atlas (HCA) from here. There are both single omics data and single cell multiomics data, and I identified which files are single cell multiomics files using the label from this website. However, I only got four fastq.gz files for an experiment (files with the same ID).
Pla_HDBR10084192_S1_L001_I1_001.fastq.gz
Pla_HDBR10084192_S1_L001_I2_001.fastq.gz
Pla_HDBR10084192_S1_L001_R1_001.fastq.gz
Pla_HDBR10084192_S1_L001_R2_001.fastq.gz
I want to further process the sequencing files (fastq.gz files) of scMultiomics using cellranger arc, but the filenames and file counts are confused. I know that just for one single cell RNA-seq experiment, there would be three files: R1, R2 and I1 fastq.gz file, so does it mean the remaining I2 file is the only file for scATAC-seq?
Or does it mean that there are other folders containing the files also for this experiment, and I should put all these related folders together to feed for cellranger arc?
Or I got the wrong labels, and these files are actually not scMultiome data but just scRNA-seq data (single omics).
May I have your comments and suggestions? Thank you very much!
Hi GenoMax , thank you very much for your help! I go through that page but still a little confused. 10x scMultiomics data would store scATAC-seq and scRNA-seq separately in different files, and for both of them, there would be 2-3 files, respectively, but here I only have 4 files in total, so may I have your suggestions if I miss download something? Thank you very much.