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Old 04-17-2014, 02:17 PM   #1
milw
Director NGS Services, Lucigen
 
Location: Madison WI USA

Join Date: Dec 2013
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Default SSPACE and number of mate pairs utilized?

hi, I've been using SSPACE with our internally made mate pair libraries to scaffold a set of E coli contigs. It seems that SSPACE is using only a few thousand of the mate pair reads to perform the scaffolding, and my question is whether that low number is related to the required linkage parameters? My mate pair libraries have a have 100,000 - 2 million paired reads, but that's probably overkill for the purpose of scaffolding 195 contigs?
thx for any help/comments!
-Scott
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Old 04-17-2014, 03:58 PM   #2
luc
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Default

The vast majority of your mates will not map to two different contigs.
In addition SSPACE also only maps to the ends of the contigs that are "in-reach" of your mate-pair insert sizes (e.g. it maps reads only to the 2kb of each contig end).
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