I about follow the “HISAT, StringTie and Ballgown” pipeline for RNA-seq analysis, but I used STAR (instead of HISAT) for mapping reads on the genome followed by Stringtie for genome-guided assembly. As you know “Ballgown” take the FPKM value (here, from stringtie) for doing differential expression analysis. But, for using DEseq or edgeR , we need raw count. As I know, the popular program for generating raw count are HTseq and RSEM, which HTseq is designed to work at the gene level (not transcript level) and RSEM accept the mapping file generated by aligning to transcriptome not genome. Could you please let me know how I should create raw count from bam file produced by STAR for further processing by edgeR analysis at the transcript level?