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Old 11-15-2011, 11:06 AM   #20
kmcarr
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Location: USA, Midwest

Join Date: May 2008
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Quote:
Originally Posted by skruglyak View Post
Sorry for the late reply. I somehow missed notification of the post. You are correct. The stats are computed after the FASTQ file is made, so this leads to the issue that you observe. Have you tried using SAV (sequence analysis viewer)? It reports a lot of valuable statistics created by RTA, including %PF.

Thanks for your feedback.

Semyon
Semyon,

Yes, it's true SAV presents some of that data, but I need the data in a format that I can parse to generate reports. This means the .xml files produced by CASAVA. The files produced by CASAVA really should properly report the number of Raw and PF clusters generated regardless of what is output to the FASTQ files.
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