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Old 10-16-2010, 01:42 PM   #8
Location: Europe

Join Date: Apr 2010
Posts: 46

Hi Simon, thanks for this. Out of interest, when you say you do 10% of a lane, how is this done? I'm not very familiar with the sequencing procedure itself, but I imagined it was an all-or-nothing, and you couldn't back out after 10%. Do you mean you are watching some results in real time (i.e. nothing to do with the GAPipeline), and making a decision to abandon if necessary after 10%? If you do abandon, does this mean the flowcell is effectively wasted? If that's what happened here (in the decribed experiment), would the authors have needed to run image analysis, etc. on partially complete reads? Wouldn't that mean that (a) they wouldn't have full length reads, e.g. they would only have 5 bases per read out of 50 potential bases and (b) they would still be paired? Thanks for your help!
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