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Old 05-21-2013, 07:34 AM   #4
Wolfgang Huber
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Location: Heidelberg, Germany

Join Date: Aug 2009
Posts: 109
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To avoid biases by caused different efficiencies of the aligner in mapping reads with different length, one might shorten the longer reads to make them all have the same length.

Otherwise, I agree with Stephen and Chad(?). The ends will justify the means, and the usefulness of your result will depend on the relative sizes of the "batch effect" caused by your experimental design and the biological effect of interest.

Best wishes
Wolfgang
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