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Old 05-28-2009, 12:14 PM   #7
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,177
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gaster,

Are you using the Roche GUI (gsAssembler) to view the 454AlignmentInfo.tsv? If so this viewer truncates the display at 50,000 lines. The file is located in the assembly subdirectory of your main project directory. You can view the entire file with a standard text editor. (Careful, if your assembly is large this file will get huge.) You will need to process the file using some sort of script to extract and calculate the coverage information you asked about (ave, min, max, etc.).
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