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Old 06-19-2011, 02:54 PM   #4
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Location: NL, Leiden

Join Date: Feb 2010
Posts: 245

First of all; probably the 'older' .txt format was also a .fastQ format. CASAVA spits out a .txt file, which is basically a .fastQ file.

Anyway; Best way to import Illumina Paired-end data is to go to 'File -> Import High-throughput sequencing data -> Illumina". Select here both paired-reads and choose your file format (.fastQ). See this link from CLC:

Illumina HiSeq data can be treated the same as Illumina Genome Analyzer data.
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