TopHat closure-search: what does it do?

[d f]

What does the --closure-search option of TopHat do?

[pbluescript]

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?

[nicolallias]

From tophat manual:

--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.

--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.

[pbluescript]

Perhaps I should be more specific.
What is the mate pair closure-based search for junctions?

[apadr007]

Did one of you guys find out what this does? I am also curious.