I'm trying to set up a scRNA-seq pipeline and run into difficulties as my sample sizes are growing (>50k cells).
Right now I create a BAM file for every cell and proces them individually, but I would like to batch multiple cells into single BAM files to prevent large amount of files. Are there any tools available that allow counting reads against a GFF/GTF file for every read group for example. Or some other tag so that I get counts for every cell without having to create a BAM file for every single cell individually.
I'm using featureCount right know, but looked at a few different tools like htseq-count and bedtools.
Thanks in advance.