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. Author manuscript; available in PMC: 2014 Jun 25.
Published in final edited form as: Methods Mol Biol. 2014;1158:123–137. doi: 10.1007/978-1-4939-0700-7_8

Figure 5. Counting reads to quantify intron retention.

Figure 5

All tracks except the gene models (TAIR10 mRNA) and cold stress RNA-Seq read alignments track are hidden. The stack height for the RNA-Seq read alignment track is optimized to allow all reads to be shown and the vertical zoom has been used to stretch the display vertically. Reads that appear to support intron retention are selected and the number of selected reads is shown in the Selection Info box. Some of the selected reads are off-screen, above the current view.