multiple outputfiles after bamtofastq for same library

[TdzBAS]

Hi,

I have a BAM file that I processed with bamtofastq. I received three folders: SC50_CR3_GRCh38_0_1_H2H33BGX2
SC50_CR3_GRCh38_0_1_HGM3WBGX2
SC50_CR3_GRCh38_0_1_HMKN5BBXX

When I check the header of the BAM file using samtools view -H, I only see entries for the library_info for H2H33BGX2. The screenshot shows only a part, but this applies to the entire header.

I assume that the others also contain reads in the BAM file, but they just don't have library_info because it is likely the same as for H2H33BGX2. It probably concerns different flow cell IDs. How should I analyze these with Cell Ranger? Can I simply concatenate the FastQ files from the different folders for R1 and R2? Or is there something I need to consider at the Cell Ranger level? If so, what is it?

Best regards,
Tolga