Let's recap what we learned yesterday:
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.
- Unspliced mappers are typically faster (particularly those using BWT).
- Unspliced mappers will miss/misalign reads that span exon-exon junctions.
- Unspliced mappers are best when mapping RNA-Seq data directly to the transcriptome.
2. Spliced mapping: HISAT2/STAR. We used STAR to map reads from two conditions C1 and C2 to our genome.
- Spliced mapping is more conducive for rna-seq data.
- Spliced alignments look different from unspliced alignments in their cigar scores ("N")
3. Pseudomapping using Kallisto: We used Kallisto to quantify transcripts using reads from two conditions C1 and C2.
- When you want to quantify known transcripts, kallisto is the fastest way to go. It skips the alignment step.
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