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Old 11-12-2010, 08:10 AM   #1
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Default Illumina file format question

I am new to the Illumina NGS system and am trying to begin analyzing some data. What are the file formats that are generated by the Illumina machine and what are the best formats to convert them into for subsequent analysis? For example, are they generated in an Illumina specific file, like .ill or something, and then to start analysis I need to convert them to .fasta or .seq or .txt ?
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Old 11-12-2010, 08:44 AM   #2
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You can find the details of illumina's output files format in the casava documentation. As for the posterior conversion to other formats, most of the downstream tools come with scripts to convert from illumina(and other platforms) to the format used by the tool (typically fastq for mapping).
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