...
- For mapping bulk standard RNA-seq to the transcriptome, use Kallisto. It's fast and accurate. BWA is also another good option, but not as fast.
- For mapping tag-seq data or single cell RNA-Seq data to the genome, use STAR.
- If interested in identifying novel transcripts, map to the genome using a spliced aligner like STAR or Hisat2.
- Mapping %: A good mapping percentage for RNA-Seq is typically 70% or above. This is provided you are mapping to a well assembled transcriptome/genome reference that is from the same species as your data.
Back to COURSE OUTLINE