Hi, I’ve got some samples that have multiple FASTQ files (i.e. 2x R1s and 2x R2s per sample). Do I need to concatenate these myself before inputting them into the pipeline or is there a way of entering this into the samplesheet? I’ve tried:

sample_id	filename_R1	filename_R2  etc……
T1	path_to_T1_R1_file1	path_to_T1_R2_file1
T1	path_to_T1_R1_file2	path_to_T1_R2_file2
T2	path_to_T2_R1_file1	path_to_T2_R2_file1
T2	path_to_T2_R1_file2	path_to_T2_R2_file2

However I get an error and when I look at the corresponding .command.log I get:

ERROR: The --sample argument must be specified if multiple samples were demultiplexed in a run folder. Available samples:
T1-SCI7T002_H2WFVDSXC
T1-SCI7T002_H3JFNDSXC

However I don't want it to consider these 2 things to be separate samples, but rather 1 sample

Hi @Rebecca Rees, you are doing this right, providing diferent fastq files corresponding to the same sample in multiple rows. Unfortunately cellranger is very picky regarding the filenames, so the filenames need to be exactly: "sample_id"__S{1,2...}_L00{1,2...}_{R1,R2}_001.fastq.gz_

Thats brilliant, thank you so much for your help!