...
We looked at mapping reads to the genome and transcriptome.
1. Unspliced mapping: BWA. We used BWA to map reads from two conditions C1 and C2 to our genome.
...
2. Spliced mapping: HISAT2/STAR. We used HISAT2 STAR to map reads from two conditions C1 and C2 to our genome.
...
- When you want to quantify known transcripts, kallisto is the fastest way to go. It skips the alignment step.
BACK TO COURSE OUTLINE