handling secondary mapped reads with rsem.

Question

[hangost2]

I try to obtain TPM values with my RNA-seq data using the rsem tool. However, I saw a lot of secondary mapped reads in transcript.bam files created from rsem at the result directory. Does the rsem tool remove these secondary mapped reads when the rsem estimate TPM or FPKM even if still remain in the transcript.bam file at the result directory?

If you would help me, I very much appreciate!! Thanks,