rRNA filtering from human RNA-seq data

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8 months ago

deniz ▴ 10

Hello, Can anyone propose tools for filtering ribosomal RNA from human transcriptomic data?

rRNA RNA-seq • 595 views

ADD COMMENT • link 8 months ago by deniz ▴ 10

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Do you actually need to do that? If your reference includes rRNA you could simply ignore those counts. If it does not include that rRNA the reads should not align.

That said you can align the data to human rDNA that you can obtain from here: https://www.ncbi.nlm.nih.gov/nuccore/U13369

ADD REPLY • link 8 months ago by GenoMax 142k

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Thank you very much for your answer! I'm working with exosomal RNA extracted from a patient's blood. As a result, I have very little input RNA and consequently a low alignment rate to the reference genome. And, because the human reference genome (GRCh38.p13) has 5S rDNA but not entire rDNA repetitions, I want to ensure that my data is free of rDNA repeats. I'm aware of few tools intended specifically to automate the removal of rDNA repeats from metatranscriptomic data (riboPicker:https://pubmed.ncbi.nlm.nih.gov/22155869/) and also plants (riboCleaner:https://academic.oup.com/bioinformatics/article/38/15/3840/6613134?login=true). I'm just curious if there is such a tool for the human transcriptome.

ADD REPLY • link 8 months ago by deniz ▴ 10

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I linked the entire human rDNA repeat sequence above. You could add it as a separate "chromosome" to your reference and then align the data to see what aligns there.

I am not aware of a defined pipeline to clean human ribosomal contamination but that does not mean one does not exist. Doing the above should be good enough.