Spliced RNA Seq Reads

We used high-throughput RNA sequencing data (RNA-seq data) from the Ecker and Mockler labs, and used alignment tools called Tophat and Supersplat to align these sequences to the Arabidopsis genome, resulting in 203,000 clustered spliced RNA-seq junctions. By clicking on the ‘?’ on the left hand side of the header of this track, you can choose to visualize labels for each RNA-seq junction (number=the number of identical RNA-seq reads that are part of a given cluster; color=blue:junctions agree with TAIR10 model; orange: junctions agree with B-List model; pink: at least one junction is distinct relative to the TAIR10 model; red: the complete RNA-seq read lies in an intergenic region relative to the TAIR10 genome annotation).