How to set sample name of fastq file output

[Yijia-Jiang]

Hi,

I used cellranger atac to run bamtofastq. The fastq output folder has "MissingLibrary". How do I set the sample name to a meaningful name instead of MissingLibrary? Also, the filename of fastq files starts with something like bamtofastq_S1_L001_I1_001.fastq.gz, how do I change the bamtofastq prefix to the actual sample name?

The command line I used is:

/software/cellranger-atac-2.1.0/lib/bin/bamtofastq file/path/to/bam/ output/directory

Thanks