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Old 04-19-2012, 12:12 AM   #3
yksikaksi
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Location: Scandinavia

Join Date: Dec 2009
Posts: 20
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Sorry for the unclear question.

The pre-filtering I refer here is view the reads with tools for example FastQC or Fastx and then trim out the so-called bad bases before mapping the reads.

The problem is the FastQC and Fastx are develop to handle reads generated from Illumina and 454 platform. The color space (csfasta) reads can't be imported directly to these tools.

Some Perl conversation scripts also having problem when convert the csfasta to fastq.

Thanks.
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