bam only containing aligned reads produced different expression profile

[TwoFlowers1]

Hello,

When we used RSEM for RNA quantification, we found that bam containing aligned and unaligned reads and bam only containing aligned reads (processed with samtools view -F 4) produced different expression profile. These two profile has Spearman correalation of 0.7. In addition, the profile produced by bam only containing aligned reads had more genes detected (TPM>0). I don't know why. Does unaligned reads were used during the quantification process?

Thank you