I have 8 BAM files from an RNAseq experiment (4 different individuals, 2 different tissue types per). The Illumina run was singled-end 50s and we have about 3.2million reads per sample.
I need to know how many counts align to the different parts of the reference genome from each sample identified by tissue type. I am trying to prep my RNAseq data to run bioconductor's DESeq2 protocol but I am stuck getting the count matrix to even start.
I have basically no programming experience; any and all help is welcome and explanations like you are talking to a child would be greatly appreciated.