The genome browser contains tracks that we can use to visualize regions of the DNA that are transcribed into RNA. This type of data can provide strong supporting evidence to the hypothesis that a certain region of a genome codes for a gene. Let's look into the RNA-seq tracks section of the genome browser to visualize this type of data. We are once again using the July 2014 gene assembly of de-molana-gaster and focusing on Contake 1. The RNA-seq tracks section contains results from sequencing mRNAs and then mapping these sequencing reads against the genome. Hence, regions with RNA-seq read coverage usually correspond to regions in the genome that are being transcribed. To visualize the RNA-seq read coverage data, click on the RNA-seq coverage link under the RNA-seq tracks section to open another window in order to specify the settings for this track. Change the display mode to full. Change the data view scaling field to use vertical viewing range setting and change the max field under the vertical viewing range section to 37. Unselect the adult males track under the list subtract section and then click submit. By unselecting the adult males option, the genome browser will only show the RNA-seq read coverage from the adult females sample. If we did not unselect the adult males option, the default would be to display both the female and male data as two separate subtracts on the genome browser. In addition to RNA-seq coverage, it is often also helpful to consider splice junction prediction data that are derived from the subset of RNA-seq reads that span two or more axons, known as spliced RNA-seq reads. To visualize these predictions, click on the axon junctions link under the RNA-seq tracks section, use the drop-down menu to select pack and then click submit. We can examine the spliced junction predictions more carefully by zooming into the 5 prime and 3 prime end of the axon. Several other tools can help us analyze spliced junctions. Top Hat is a program that can identify spliced junctions without relying on a database of known junctions. Top Hat first identifies potential axons by mapping segments of RNA-seq reads to the genome. Because RNA-seq reads are short sequences derived from processed mature mRNA, they will often align continuously with an axon. However, some RNA-seq reads will span multiple axons, thus containing valuable information about spliced sites. Top Hat builds a database of possible spliced junctions followed by mapping the actual sequencing reads against these predicted junctions. This method allows us to find novel spliced sites, aligns RNA-seq reads to the genome assembly, and then analyzes the mapping results to identify the spliced junctions between axons. To illustrate, let's view the RNA-seq data for a different drosophila species. Click on the genome's link on the main menu bar to return to the genome browser gateway page. Change the genome field to D biomepies. The assembly field to April 2013, B-C-M-H-G-S-C-D-B-I-A underscore 2.0, enter TRA-PA into the search term field, and then click Submit. We are now navigating to the genomic region that contains the presumed TRA-Ortholog in the drosophila biomepies whole genome assembly, and will examine the evidence tracks for the presumed orthologue. Scroll down to the RNA-seq track section, and then change the display mode for the mod and code Top Hat junctions track to pack to view the individual spliced junctions. After clicking Refresh, we now see a single track with the collection of all Top Hat spliced junctions predictions from the mixed embryos, adult female, and adult male samples. In order to create this track, spliced junctions from the different libraries are filtered and then merged together. The predictions are color-coded to indicate the number of spliced RNA reads that support the predicted spliced junction. Red indicates that there are more than 1000 spliced RNA-seq reads supporting the junction, followed by brown, pink, green, blue, and black in descending order, with black corresponding to fewer than 10 reads. Several other evidence tracks are available under the RNA-seq track section. You may click on the track title link above the display mode drop-down list to learn more about how that evidence track was created, and the display convention used by that particular track.