I tried this approach. No problems to download the BAM file nor to install bamtofastq v1.4.1.
However when running bamtofastq I have warnings :
WARNING: no @RG (read group) headers found in BAM file. Splitting data by the GEM well marked in the corrected barcode tag. Reads without a corrected barcode will not appear in output FASTQs
The BAM format is not recognized as I also have the error message :
Unrecognized 10x BAM file. For BAM files produced by older pipelines, use one of the following flags: --gemcode BAM files created with GemCode data using Longranger 1.0 - 1.3 --lr20 BAM files created with Longranger 2.0 using Chromium Genome data --cr11 BAM files created with Cell Ranger 1.0-1.1 using Single Cell 3' v1 data
As I do not have any info about the origin of this BAM file I tried with the 3 options proposed.
The only one that was recognized was --cr11 but it did not create any file.
It looks like I am in the case of a BAM file coming from an alternative pipeline.
Hmm, from https://www.ncbi.nlm.nih.gov/sra/?term=ERX5671923 -- it seems that only one FASTQ file (the 91-bp biological sequence) is available. Unfortunately, that means the barcodes and UMI sequences are not available. Therefore, it's not possible to just use that one file with any tool. You'd need to find some way to obtain the other FASTQ file.
Thank you for your answer. It corresponds exactly to the answer I was afraid of. I have to check more deeply but it looks like the same issue applies to all run of all libraries from this Fly Cell Atlas experiment :'(