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 transcriptome.

• • 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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