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Old 08-07-2015, 01:08 PM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

His advice still holds. Particularly when you are looking at things where you expect a large difference from the reference (tumors, bisulfite, etc) it's bad practice to map only to the part you're interested in. There is no way to avoid the false positives that incurs, so your results will be untrustworthy.

If alignment is too slow, you can use a faster aligner, or tweak the settings of the existing aligner, or use a computer with more cores, or split up the data and map on multiple computers. How are you doing the alignment?
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