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

Join Date: Feb 2008
Posts: 7,080

You can use the "filter" mode for "" 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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