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What does the --closure-search option of TopHat do?
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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? -
From tophat manual:
I believe it has to work with the following, but haven't test yet.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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Perhaps I should be more specific.
What is the mate pair closure-based search for junctions?Comment
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Did one of you guys find out what this does? I am also curious.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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