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Old 09-04-2020, 10:09 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080
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You can use the "filter" mode for "bbduk.sh" from BBMap suite for this. Download the human rDNA repeat sequence. Reads that match rDNA can be filtered away from your data. A guide to use bbduk is available here.

If most of rRNA has been depleted from your sample there is not much you can do.
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