multiple outputfiles after bamtofastq for same library

[TolgaDuz]

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

[bread1006]

I have met the same question， may I ask how did you solve the issue? Can I simply concatenate fastaq files from the different folders?

[RoelsJana]

I just encountered something similar
From 1 bam file I got 2 folders:
├── SampleName_1
│   ├── SampleName_0_1_HFFTYDMXY
│   └── SampleName_1_1_HFFTYDMXY

[RoelsJana]

@bread1006 I just found that for me HFFTYDMXY is connected to my sequencing run
So if you are getting multiple folders where everything is the same except for the string of 9 characters, you migth have data from multiple sequencing runs.
But I haven't found out why I'm having 2 folders yet

[bread1006]

@RoelsJana Here is my situation. One BAM file transferred into 4 file folders, One file folder contained 4 fastq files (this is because my sequence run is X10 Genomic) . Anyway, thanks for your reply, I possibly won't handle it anymore.