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A new track will then appear containing junction features bracketing introns (see below). Labels report the number of spliced alignments that supported the junction.  Each inferred intron appears as a thin line connecting two blocks, one on either side of the line. The width of these "flanking" blocks indicate the number of bases you entered in step 3 above, unless you selected the "Find Junctions (TopHat)" option. If you chose that option, then FindJunctions will create flanking blocks as large as the longest aligned region detected from any of the sequence read alignments. For example, if there was just one sequence that aligned across an inferred intron with 20 bases on either side of the intron, then the blocks will be 20 bases in size. The name "TopHat" comes from a software program with similar behavior. TopHat is an RNA-Seq sequence to genomic assembly sequence alignment tool that created junction feature files (called "junctions.bed") using sequence read alignments. For more information about TopHat, visit the TopHat Manual.

Find Junction 

Using FindJunctions from the command line

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