Expression analysis of miRNAs with normal RNA-seq data without small RNA-seq data
Hello everyone.
Can I do expression analysis of miRNAs with normal RNA-seq data without small RNA-seq data? Which path should I choose for known miRNAs and unknown new miRNAs?
Thank you for your interest
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ATpoint
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Burak Muhammed •
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Burak Muhammed •
1 answer
My personal opinion is no. Normal RNA-seq both uses RNA extraction kits that enrich for RNA fragments with sizes above miRNAs and the library prep also enriches for fragments of >~ 200bp, hence any miRNA you pick up should be considered noise. It is imho unreliable for known and especially unreliable for de novo detection of miRNAs. Do miRNA-seq.
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Cross-posted: https://bioinformatics.stackexchange.com/questions/19622/expression-analysis-of-mirnas-with-normal-rna-seq-data-without-small-rna-seq-dat
Not surprisingly they tell the same thing. It is good practice to indicate cross-posts by providing links, that avoids double-effort for members in both communities.