Why have fastqc and trimmomatic been deprecated and what should I use as a replacement?
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None of the two has been deprecated afaik. Where did you get this information?
edit: I see what you mean now, the tool panel on usegalaxy.org seems mixed, we will fix it. The tools are not deprecated, just positioned wrongly in the panel.
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Thank you, marten.
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It has been fixed, thanks for reporting it.
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