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Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?

I have some small RNA seq data to analyze miRNAs. I trimmed the adaptors, selected reads of 18-25 nt, mapped the reads to the genome, detected novel and conserved miRNAs using mirdeep2. I’ve already done DE analysis and target predictions. However, I realized that I did not remove rRBAs, tRNAs, mRNAs, and other types of ncRNAs. I know I can filter them out using the Rfam and NCBI database. But is it really a necessary step to filter them out? It will take me a long time to do these analysis.

mirdeep2 mirna rna-seq
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updated by kuttibiotech2009 • kuttibiotech2009 • written by tianshenbio tianshenbio

Dear sir, I also would like to remove rRNAs, tRNAs, mRNAs, and other types of ncRNAs using Rfam. I have no idea about it. can you please share some links related to this?.

Thanks KAMALAKKANNAN R

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written by kuttibiotech2009 • kuttibiotech2009

Do you want to remove these by using a standard identifier (e.g. from Pfam) or based on sequence?

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written by GenoMax GenoMax

Thanks for your reply sir, I want to go with sequence based one

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written by kuttibiotech2009 • kuttibiotech2009

2 answers

Rfam sequence files: https://docs.rfam.org/en/latest/ftp-help.html

You could also download the sequences you need for a species from: https://rnacentral.org/

Then it would be a matter of creating indexes and aligning your data.

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written by GenoMax GenoMax

One approach is to make sure all the 'unwanted' RNAs exist in your reference genome and then exclude these from any downstream analysis. If you're aligning to human you might want to try the T2T genome as you might have better luck discovering novel miRNAs in this genome.

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written by noodle noodle

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