If you are following certain RNA-Seq workflows, the wizard includes the Set Contaminant screen. The screen prompts you to remove rRNA sequences if they are present. We highly encourage doing so, as these sequences can represent up to 80% of the reads in a de novo transcriptome data set and can swamp the assembly due to their large numbers.

Check Scan for rRNA contamination to enable the three add/remove sequence buttons on the right. You will then need to specify rRNA sequences here, as described below. Typically, you will add reference sequence(s) from a 16S rRNA database (e.g., Silva, Greengenes Ribosomal Database Project, etc.

See the following topics to learn how to:

Click Next > to proceed to the next wizard screen or < Back to return to the previous screen.

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