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Old 06-01-2012, 12:13 AM   #1
Gorbenzer
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Location: italy

Join Date: Apr 2012
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Default 200bp kit with 316 chip + question: larger fragments selection

Hi everyone,
i have a couple of questions:


1.
We recently started to use 316 chips with 200bp kits and we encountered two problems: the first is that using the 200bp kit, the PGM output has a peak at 150bp (as show in the graph) and this happens with both 314 and 316 chips. The second problem is that using the 316 chip results in an output of 30Mbp or lower (while using the 200bp kit with a 314 works fine). Note: we are following the new protocol for 200bp kits and using 316 chips bought as they where available on the market.
Anyone have suggestions?


2.
Having the 150bp read lenght problem using the 200bp kit made me think: anyone ever tryed to create a library with fragments longer then specified by the kit?
i.e. 250bp for 100bp kit or 350bp for 200bp kit?



As always, thanks for your help

Last edited by Gorbenzer; 06-01-2012 at 12:39 AM.
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Old 06-08-2012, 09:13 AM   #2
snetmcom
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Did you do any kind of QC on your libraries to validate your average insert length? The protocol recommends an average insert around 250-270bp, so you should have plenty of room for 200bp reads.
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