^ I have not but this was something that was just suggested to me and I might give it a try. For generating the matrix file, how many tiles do you think is adequate? And do you do all cycles or can I shorten that as well?
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I usually pick 10-20 tiles and then run for 25 cycles. I try to avoid picking tiles from the flowcell edges as they're more prone to have problems. It runs pretty fast and gives you a Bustard.xml that you can check it to see if the pass filter/etc looks reasonable before doing a full pipeline.Comment
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Does adding the PhiX spike-in to each sample have the same effect as adding an ERCC control? Ambion offers this ERCC control to help with accurately quantify transcript levels, but I'm not sure if I need to invest in this addition or not... Any thoughts?
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