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- Check the sizes of the blocks for the Find Junctions tracks (it should match the value you entered); the find junctions (tophat) results will not all have the same block size.
- Verify that the count above each junction is equal to the number of reads that matched that gap.
- Find someplace where the matching Find Junctions operation using value 5 and value 10 have different values. Identify the read(s) that matches that junction, and where where one side of the read is between 5 and 10 bases.
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