I have 4 sample of rna seq data(control and disease). i did alignment with STAR and RSEM to get the count matrix. now i want to know the size of isoforms in both cases of particular gene? how can i get this?
You simply look it up in the the annoation you used tu build the index for RSEM. If you used a fasta file you can look up the isoform length (as it is the same length as the number of nucleotides for that entry). If you want the number of exons you will have to download the corresponding GTF file and extract the information from there.