What does the --closure-search option of TopHat do?
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From tophat manual:
Code:--closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)
Code:--min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50. --min-closure-intron The minimum intron length that may be found during closure search. The default is 50. --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.
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