Good Afternoon! I am attempting to run the scrnaseq pipeline on an inDropsv3 dataset, but am having trouble finding the correct format for my sample sheet. I am inheriting this data from a few years back, and as such, am just interpreting what I can from the files given to me. There are 4 fastq files associated with each sample, which leads me to conclude the version chemistry. However, from what I learned online, the scrnaseq pipeline's kallisto functionality only allows for 2 fstq files input per sample, which obviously doesn't match up with the data I am seeing. Is there perhaps a dev branch of the pipeline or an older branch that is compatible with this data format? Thank you!

Hey, the most related prior conversation on this topic that I was able to find is this. So it seems that the 4-fastq format that is required for inDrops is not currently supported. Sorry about this! Hopefully we can add support soon