Quantify reads that fall within introns

[harshini-c]

Hello,

I am trying to do isoform level analysis on my nuclear RNAseq dataset. I used STAR to align the reads and want to use RSEM to quantify expression levels. I modified the GTF file to include intron information in the STAR alignment step. My question is whether RSEM will be able to quantify both primary and mature transcripts?

Alternatively, what steps would you recommend I take to make sure that intronic reads are also counted?

Your inputs in this regard will be very helpful!

Thank you.