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Old 04-11-2012, 06:24 AM   #12
biofreak
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Location: USA

Join Date: Jun 2011
Posts: 44
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I have specified separate output dir which shows all the 6 folders for the 6 lanes. Each one contains just the csv file for the respective sample but no zipped fastq files. My command is:

nohup ~/home/CASAVA_v1.8.0/bin/configureBclToFastq.pl --force --input-dir \
~/home/HU_02_HPDCAZX/Data/Intensities/BaseCalls \
--output-dir /home/HU_02_HPDCAZX/Data/NoIndexUnaligned --sample-sheet ~/home/HU_02_HPDCAZX/Data/Intensities/BaseCalls/SampleSheet_NoIndex.csv > nohup_first.out
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