I'm working with RNA-seq data and I'm already done with alignment(i.e. I have the BAM files). My question is:
Is there a tool or script which can quantify the aligned reads on the basis of their types, i.e. mRNA, lncRNA, miRNA etc just from the alignment files (BAM ) and annotation files (GTF/BED). I need the data in form of number of aligned reads belonging to each RNA type. The reason I need that data is because I want to plot the population of each type for each alignment file I have.