Hi there,

I'm sorry for the newbie question but I'm confusing and getting lost in my thoughts.
Having `WES` data, until the moment I have been using `DNASeq` aligner such as `BWA MEM`. But I'm wondering whether it makes sense to use `RNASeq` mapping algorithm (`STAR`...) or not and why. 

For other hand lets say that I want to consider the alignment of the reads against only the exons of some genes. How this would affect the aligner algorithm decision?

Thank you in advance,
Stick with a DNA based aligner like BWA (recommended in the [GATK best practises][1]). DNA sequencing (such as WES), is sequencing DNA fragments pulled down by a pre-designed capture kit, whereas RNA sequencing is sequencing the actual mRNA. When aligning RNA reads, the aligner (STAR, HISAT2, etc) will expect reads to split across exons, as such the appropriate penalty for that is tuned - that sort of event shouldn't happen with DNA. 


  [1]: https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS