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Old 01-27-2019, 04:34 AM   #50
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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@Maya: Can you explicitly add -Xmx128g (is that what you are asking for) threads=24 in your bbnorm.sh command?

I also don't understand this part: in=$fastq_DATA/petrosia_SE.fastq out= out2=petrosia_SE_normalized_ecc.fastq There should just be one "out="?

Normalizing RNAseq data is not appropriate. You are going to lose vital count information. See the section on "When not to normalize" in BBNorm guide here.

Last edited by GenoMax; 01-27-2019 at 04:38 AM.
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