I am wanting to normalize my RNA-seq data without running a differential gene expression on any of my samples. I can easily run HISAT2 and then sam/bam counts to get a count matrix but I assume this is raw counts? How do I then, at the very least, normalize those counts to account for library size etc?
Generally one does this in comparison to other samples (e.g., with edgeR or DESeq2 in R). This is generally the most robust method.
Thanks for your response. Basically i have rna seq fastq files on single cells and im not wanting to draw any comparisons on them yet. I'm just hoping to normalize and come up with a table of gene expression. Does edgeR or DESeq2 do that without running differential comparisons? Sorry if this is a really naive question