Hello everyone, I have single end sequence fastq files that were processed using cellranger. Now I need to align them using cellranger count function. But being single end, the naming convention followed could not be standard. Is there a way to do so? I tried using SRR9320581_S1_L001_R1_001.fastq.gz file convention, but it gave pipestance failed error.
Any help is highly appreciated. Thank you