Introduction to Alignment
Module 2 - Key concepts
- Splice-aware alignment, SAM/BAM format, SAM flags, CIGAR strings, SAM sorting, etc.
Module 2 - Learning objectives
- RNA-seq alignment challenges and common questions
- Alignment strategies
- HISAT2
- Introduction to the BAM and BED formats
- Basic manipulation of BAMs
- Visualization of RNA-seq alignments in IGV
- Alignment QC Assessment
- BAM read counting and determination of variant allele expression status