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Old 03-09-2011, 05:55 AM   #3
nicolallias
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Location: France

Join Date: Jan 2010
Posts: 23
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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)
I believe it has to work with the following, but haven't test yet.
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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