I have aligned reads from STAR with
--quantMode TranscriptomeSAM GeneCounts, which then outputs the files
ReadsPerGene.out.tab. I'd ideally like a piece of reputable software to calculate the TPMs from these files (plus any necessary annotations file). Can anyone recommend me the correct tool here and briefly describe what I need to get it working?
A further naive question, but if I want to do gene expression analysis i.e. differential expression or some other modeling of the normalized counts, do I ever even need the
Aligned.out.sam file? I don't know what this is used for.
EDIT: I am continually coming across RSEM as a tool that takes as input
Aligned.toTranscriptome.out.bam and outputs normalized counts. I will look into this.