+=over
+
+=item B<output_plot_file>
+
+This is a pdf file containing all plots generated. If a list of transcript ids is provided, each page display at most 6 plots in 3 rows and 2 columns. If gene ids are provided, each page display a gene. The gene's id is showed at the top and all its transcripts' wiggle plots are showed in this page. The arrangment of plots is determined automatically. For each transcript wiggle plot, the transcript id is displayed as title. x-axis is position in the transcript and y-axis is read depth.
+
+=item B<sample_name.transcript.sorted.bam and sample_name.transcript.readdepth>
+
+If these files do not exist, 'rsem-plot-transcript-wiggles' will automatically generate them.
+
+=item B<sample_name.uniq.transcript.bam, sample_name.uniq.transcript.sorted.bam and sample_name.uniq.transcript.readdepth>
+
+If '--show-unique' option is specified and these files do not exist, 'rsem-plot-transcript-wiggles' will automatically generate them.
+
+=back