Ribosomal depletion percentage
Hello, I want to observe the percentage of ribosomal depletion in my fastq files that were sequenced with NextSeq, how can I do that? I have never done this before. Is there a tool or script I can use?
Thank you
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You can try riboPicker.
In addition to riboPicker, you can also use SortMeRNA and BBDuk with the "ribokmers.fa" file. This later is my preferred approach, as it is really fast.