Before proceeding with the analysis of raw FASTQ files, it is important to appropriately name the files. While different laboratories and analysis procedures may have their own naming conventions, it is generally recommended to adhere to the following basic requirements:

The file name should clearly reflect the sample source, including sample number, organization source, and processing method. Use characters like underscores or dashes to separate the information. For example: Sample1_Blood_RNAseq_R1.fastq(.gz) and Sample1_Blood_RNAseq_R2.fastq(.gz).

Include key experimental information in the file name, such as sequencing type and platform. Again, use separators like underscores or dashes. For example: Sample1_Blood_RNAseq_Illumina_PE.fastq(.gz).

Ensure that each FASTQ file has a unique name to avoid duplication or overwriting of existing data. You can use unique filenames or include timestamps. For example: Sample1_Blood_RNAseq_Illumina_PE_20220331.fastq(.gz).

It is important to maintain consistency in the naming rules and follow common conventions to facilitate data management and sharing. Additionally, some analysis software and tools may have specific requirements for filename formats, so it is advisable to consult the documentation of the corresponding software to determine any specific filename requirements before starting the analysis. For the naming method of Mozhuo's single-cell V(D)J input file, please refer to the 8th question.