To evaluate the aligned reads for a gene or isoform of interest from an RNA-seq experiment, you may select an entry in the ArrayStar Gene or Isoform tables and display the corresponding sequence reads in SeqMan Pro’s Strategy View.
To do this:
1) Close any instance of SeqMan Pro running on your computer.
2) Create or open an RNA-Seq gene expression analysis project in ArrayStar.
3) Open the Gene or Isoform Table and locate a row with a gene/isoform of interest. Then select a row and choose File > Send Selection To > SeqMan Pro from the main menu; or right-click on the row and choose Send Selection to SeqMan Pro from the context menu.
4) (multi-experiment project only) If your projects contain multiple experiments, the Choose Experiment dialog opens. Choose the experiment for which you wish to view the gene/isoform and press the OK button.
SeqMan Pro will launch and load the contig containing the selected gene/isoform. In the Summary View, the contig will be named as “[project name] [contig name]” (e.g., NA12878_control NC_000001). The Strategy View and Feature Table for that contig will also open to display the point where the gene/isoform is located.
•If you now send another gene/isoform on the same contig from the same experiment, SeqMan Pro’s Strategy View and Feature Table will move to the new position.
•If you send another gene/isoform from a different contig from the same experiment, or the same contig from a different experiment, SeqMan Pro will add a new entry to the Summary View and open the corresponding Strategy View and Feature Table.
Note: This functionality is also partially available from ArrayStar’s Exon table. SeqMan Pro will navigate to the correct position in the Strategy View; however, the Feature table will not highlight the corresponding gene/isoform.