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Old 05-13-2013, 08:36 PM   #4
Jeremy
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Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
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Like I said, you only need to cut if doing a de-novo assembly because the non-randomness of the start of the reads could cause problems in assembly, if just aligning to a genome then the read should align anyway. The non-randomness of the start is usually caused by the 'random' primers used to make cDNA. The stretch of Gs or As are either bad quality reads or legitimate stretches of repeats that happened to get sequenced, either way the SLIDINGWINDOW option seems to remove them.
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