Goby alignments can contain splicing information. Splicing information is used to connect parts of an alignment that map in different parts of the genome, such as when a read maps through an exon-exon junction and aligns on either side of an intron.
- Download the latest version of GSNAP, configure and compile it with Goby support.
- Run a GSNAP alignment with the -s option, writing the result to Goby alignment format (see -A option).
- Load the alignment in IGV. Splice information is automatically detected and displayed visually. The following snapshot provides an example of what the display conveys (note that some reads map through more than two exons):