Does any one know any paper or personally compared the results of the following approaches ?
Mapping RNA-Seq reads to transcriptome fasta using bowtie2 and quantifying using RSEM or other tools.
Mapping RNA-Seq data to genome fasta using STAR and quantifying using featureCounts.
In first case, there is less chances of finding multi-mapped reads because we focus only on transcribed regions and ignore rest of the genome. Don't know how often it's a problem or meaningful.
Some of the data I am looking at shows differences in quantifications coming from two methods for some important genes, so just thought if some one has more insights into it.