Running cellranger on multiple files when R1 and R2 fastqs are in multiple subfolders

Question

[abbas89]

Hi, I have downloaded a public dataset and would like to run cellranger count on it. The main folder is CNP000460, containing multiple samples, such as CNS0094872, this sample folder has several associated subfolders, each subfolder contains a fastq file from a separate lane, either R1 or R2. I am truggling to run cellranger on this data as it is. one solution would be to move all the fastq files into one folder only, but I was wandering if there was a more straightforward solution without changing the structure of the folders.

Answer 1

[ATpoint]

CellRanger is very picky in these things and it (by best knowledge) expects data in a single folder. My first approach would be to simply symlink them all into a single folder and run CR on that.

[swbarnes2]

I've used symlinks to run data from two separate runs together. I don't think current versions of cellranger care about the index files any more, so you don't have to worry about making symlinks for those.

[ATpoint]

Agreed. I never have index files present during the run and either delete them or compress to CRAM and store away somewhere. They're not required.