What is the best aligner for stranded RNASeq

Question

[tarek.mohamed]

Hello,

What is the best aligner for stranded RNASeq?

Thanks

Answer 1

[rpolicastro]

If you only need to quantify expression at the transcript/gene level, use Salmon or Kallisto. If you need to align reads to the transcriptome or genome go with STAR.

Answer 2

[jkim]

Not sure about the best aligner, but there are some aligners that widely used, such as STAR or HISAT2. I saw some article comparing aligners using simulating data. If I remember it correctly, GSNAP and STAR did pretty good jobs.