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?
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