The class began with learning about different plant tissues and how it develops. This is important in order to understand the differences that we might fight when we analyze our data. Then we began exploring different sequencing technologies and their different purposes. We look at different RNA-seq data or meristems and leaf samples of Arabidopsis and tomato plants. We were then exposed to what is a computer supercluster, how to navigate it and make use of its power. We then start to adapt different codes and perform different tasks using programs such as FastQC, STAR and Salmon. The products of the scripts or the data we retrieved were then analyzed to observe the differences or similarities between tissues.
Species: Solanum lycopersicum var. cerasiforme (cherry tomato)
Germplasm/cultivar/accession: Peacevine
Why: Cherry tomatoes are a different subspecies than M82. How do you think our RNA-seq data will align to a different subspecies?
Directory: TBA
Publication/website: Graph pangenome captures missing heritability and empowers tomato breeding | Nature
Download link: Index of /tomato/ftp/ (agis.org.cn)
Sample GID: TS545