Currently lost between contigs, scaffolds and chromosomes due to positionally sorted scRNAseq bam files

Question

[nyxtoviopouli]

Hello everyone,

I have downloaded some scRNAseq bam files from EGA, but the contents of the files look like this (header + first 3 rows of a random bam file, accessed with samtools):

@HD    VN:1.6    SO:coordinate
@SQ    SN:AAACCTGAGAACAACT-1_contig_1    LN:685
@SQ    SN:AAACCTGAGAACAACT-1_contig_2    LN:673
@SQ    SN:AAACCTGAGAACAACT-1_contig_3    LN:478

There is clearly something wrong or missing here. So the question is, are these files analyzable at all, and if no, what info should I expect to see in the bam file of a scRNAseq alignment? Also, is CellRanger the only option for analyzing this kind of data? Thank you in advance for your time.

[ATpoint]

I have never looked at scRNA-seq headers actually but if this is a CellRanger bam file then simply use the 10x Chromium bam2fastq utility to restore the original fastq files. From there you have full control over the preprocessing. CellRanger is one option. STARsolo, alevin-fry or kallisto-bustools are others that perform well.

[GenoMax]

That is an odd header. What kind of data is this? Can you link the EGA accession (if it is public)? Generally cellranger should produce BAM files aligned to the genome reference and files have a "normal" header. It looks like these are cellbarcodes attached to something.