Before analyzing raw FASTQ files, proper naming is essential. While different labs and analysis pipelines may have varying naming conventions, the following basic requirements should be met:

● The filename should clearly reflect the sample source,including sample ID, tissue origin, and treatment method, separated bycharacters such as underscores or hyphens (e.g.,Sample1_Blood_RNAseq_R1.fastq(.gz) and Sample1_Blood_RNAseq_R2.fastq(.gz)).

● The filename should include key experimental information, suchas sequencing type and platform, separated by characters like underscoresor hyphens (e.g., Sample1_Blood_RNAseq_Illumina_PE.fastq(.gz)).

● The filename should uniquely identify each FASTQ file to avoidduplication or overwriting existing data. Unique filenames or time-stampednames are recommended (e.g.,Sample1_Blood_RNAseq_Illumina_PE_20220331.fastq(.gz)).

Naming conventions should be consistent and follow general naming practices to facilitate data management and sharing. Some analysis software and tools may require specific file naming formats, so it's important to review the relevant software documentation before analysis to determine exact file naming requirements. For naming conventions specific to MobiVision single-cell V(D)J input files, please refer to question 8.