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-   -   TopHat closure-search: what does it do? (http://seqanswers.com/forums/showthread.php?t=7793)

d f 11-10-2010 11:00 AM

TopHat closure-search: what does it do?
 
What does the --closure-search option of TopHat do?

pbluescript 03-09-2011 05:32 AM

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 03-09-2011 05:55 AM

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.


pbluescript 03-09-2011 05:57 AM

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

apadr007 03-15-2012 12:28 PM

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


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