multiple outputfiles after bamtofastq for same library

Question

[Tolga]

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

[Pierre Lindenbaum]

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Answer 1

[GenoMax]

It probably concerns different flow cell IDs

Yes that is correct.

You can do the following if the files are in different folders when you specify --fastqs option.

If the files are in multiple folders, for instance, because one library was sequenced across multiple flow cells, supply a comma-separated list of paths.