The key idea in Reference-base Expression analysis
Reference-base Expression analysis: the key idea¶
Map reads to a reference genome with aligners¶
- TopHat
- TopHat2
- HiSat
- HiSat2
- STAR
→ These aligners are “splice aware”
→ They generate a BAM Alignment file
Use a read counting software and annotation information (GTF, GFF3, BED, …) to count the read spanning a gene / transcript¶
The input file for this counting software is the BAM Alignment file