BAM to gene expression matrix (UMI counts per gene per cell),10X I am trying to reproduce some results of a scRNASeq experiment. However I am new to the server-side aspect of such analyses and am very confused at the moment.

The data provided by the authors of the paper is in .BAM format and from there I wish to derive a gene expression matrix (UMI counts per gene per cell). The authors stated that they did this using the 10X genomics pipeline, however it seems that .BAM outputs are sort of the "final version" of the pipeline and, the pipeline only really deals with truly raw sequencing files (bcl/fastq).

I have considered converting it back to fastq format and following the pipeline from the beginning, but it just seems like I would be moving backwards by doing such.

I have also found some R packages that can integrate BAM files in the environment like Rsamtools, but I would much rather do this on the server and then upload a csv into R for the downstream analysis as the files are +60GB each. 

Essentially I am just asking for some advice, or a vignette/article I can read that would clear up how to proceed with the BAM outputs to derive the gene expression data. I have already read the cellranger pages on the 10X genomics website but they were of no help in answering this quesion. 

Thank you for your time,
You should be able to parse out what you need using the tags in the .bam.  10xGenomics' website says what tags they add.

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam

Going backwards would also involve parsing the tags, because you have to make two fastq files, and a simple bam -> fastq pipeline won't do that correctly.