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Old 02-08-2010, 10:08 PM   #3
Cole Trapnell
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Location: Boston, MA

Join Date: Nov 2008
Posts: 212
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The fact that TopHat thinks the seed length is 43bp is concerning. The default is 25, and it shouldn't be different unless you specified --segment-length, which you didn't. TopHat currently requires that FASTQ files have records where all of the nucleotides for each read appear on a single line. Same goes for the quality strings - all the quality characters need to be on one line. This is a limitation I haven't had time to fix yet. Can you verify that your FASTQ file is formatted this way?
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