Here are the few steps you mat try when opening RNAseqViewer for the first time after installation (see Installation page). The data used in this quick tutorial can be downloaded on the download page.
First load some reference gene annotations. Loading datasets is made using the Datasets menu.
You can choose to load the annotations dataset hg18.txt provided in the sample data package. The result should look like this:
The track list now has one item, corresponding to the newly added annotation track. The default position is the very beginning of the track, which is chr1:1-32 on this example. You can either search for a gene, input coordinates or navigate along the track to see other regions (see Navigation page).
Let’s enter the gene name SLC25A6 in the search field.
Two annotations have been found in hg18.txt. Choose the one on chromosome Y and click on the button “See >>”, then you can close the search dialog. Now we can see the gene SLC25A6 on chromosome Y. Some information appear in the “Items information” box when pointing on the gene.
Now we can add more data like through the “Datasets” menu. For instance, we can load the read alignment file SRR057629.bam and the splicing junctions file SRR057629-junctions.bed.
Icons in the “Track list” let you change the type of view of each track. You can also explore the different menus and buttons to further customize your visualization.