I am analyzing the RNAseq data to quantify transcript variants for a specific gene. Ensembl database shows that it has 11 transcripts (splice variants). First I aligned the RNAseq data using Kallisto to quantify transcripts. In second method, I aligned RNAseq data against human genome, and then counted the features (Transcrip IDs) from sorted bam files using subread . There is huge difference between raw counts of transcripts that specific gene. What method is more reliable?