cellranger count help for fastq files with different sample order/number

Question

[Lynn]

Hello,

I am trying to analyze my dataset of fastq files of one sample with different sample order like Test1_S1_L001_R1_001.fastq.gz, Test1_S2_L001_R1_001.fastq.gz and Test1_S3_L001_R1_001.fastq.gz. I am not sure about that if I should specify the sample order？

Answer 1

[GenoMax]

Looks like these are cellranger mkfastq demultiplexed files. The naming you show here does not make sense though. Test1 sample should not have different S*. See this link for help: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input

[Lynn]

Thank you.