Ribosomal depletion percentage
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3.3 years ago
Pin.Bioinf ▴ 300

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

ribosomal depletion RNA-Seq • 604 views
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You can try riboPicker.

The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

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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.

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