I have my first single celled dataset and there are about 2000 single cell transcriptomes. I usually keep the sorted.bam files [STAR -> samtools sort] but I'm a little limited on space at the moment.
I'm wondering if I should keep the BAM files after I use featurecounts for mapping? As a backup, I've put all of the read identifiers into a list.
What good use cases can I use for RNA-seq bam files after they have been counted?
In metagenomics, I use these for coverage estimates and binning pipelines but I haven't thought of a good reason to keep these other than having files for backup in case I lose the counts table.