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Old 11-10-2010, 11:00 AM   #1
d f
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Default TopHat closure-search: what does it do?

What does the --closure-search option of TopHat do?
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Old 03-09-2011, 05:32 AM   #2
pbluescript
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I'd also really like to know what this does. I have some sequence data from PE reads with a range of fragment sizes. If some of the reads meet the criteria for the expected inner distance between mates to be <= 50 bp, but some do not, does anyone have an idea how this would affect mapping?
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Old 03-09-2011, 05:55 AM   #3
nicolallias
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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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Old 03-09-2011, 05:57 AM   #4
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Perhaps I should be more specific.
What is the mate pair closure-based search for junctions?
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Old 03-15-2012, 12:28 PM   #5
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Did one of you guys find out what this does? I am also curious.
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junction detection, rna-seq, tophat

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