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- In an actual RNAseq analysis, you might want to trim stray adaptor sequences from your data using a tool like the FASTX-Toolkit, FAR, or FAR cutadapt before aligning.
- You can get a lot more information from RNAseq data than you could from a microarray experiment. You can map transcriptional start sites, areas of unexpected transcription, splice sites, etc. - all because you have full sequence information that we have barely used in this example.