Originally posted by skruglyak
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I really appreciate that Illumina has been so responsive to customer feedback with regard to refinement of the CASAVA pipeline and I really hate to keep coming up with more things to tweak/change, but...
I just ran my first data set through the new 1.8.2 pipeline and truly appreciate the PF only default and --fastq-cluster-count 0 options, however I noted what I consider a bug in some of the summary files produced by CASAVA. Some summary files (e.g. Flowcell_demux_summary.xml) report the number of PF clusters/bases for for both raw and PF counts. Other files (e.g. BustardSummary.xml) appear to correctly report raw and PF.
Thanks again.
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