small rna length distribution
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2.4 years ago
bioinfo_ga ▴ 20

I am performing small rna analysis and using srna-workbench for data trimming (Adaptor trimming and length filtering). After length trimming (16-40 bases) i am observing the distict reads are maximum of 32 bp whereas for small rna peak is observed at 18-22bp. What could be the reason?

mirna • 1.3k views
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Hi ,

How do your performed your trimming step with list of adaptor sequence ?

What tool do you used ?

Are you sure you can t have 32 bp RNA possible ? I was thinking in Piwi RNA for exemple .

Best

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I have used small rna workbench tool and used inbuilt adapter (LMN_3). I went through published papers of which almost all have reported the same trend (18-22bp). I checked for piwi RNA also but it is <0.02% in my data.

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ok may be just check with fastq if you have a correct nuclear acid repartition in your trimmed reads.

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You would not expect very much piRNA unless you are deriving your sequencing samples from the core reproductive organs.*

*Assuming you aren't researching plants

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Hello bioinfo_ga,

What's your experience with srna-workbench? I am trying to analyze my plant srna seq data with it. But I don't know how to install it in my windows system :(. Could you share your experience with me? Appreciate sincerely.

Wei Xu

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2.4 years ago
benformatics ★ 2.6k

Depending on the protocol used (which you did not mention so it is hard to tell) you could have degradation products remaining from turn-over of endogenous mRNA.

However, a smallRNA peak at 18-22bp makes sense... at least in animals as this would correspond to high levels of miRNA and/or siRNA. Generally smallRNA have the following ballpark size ranges (you should investigate what is expected for your organism of interest):

  • 21-22 nt siRNA
  • 21-23 nt miRNA
  • 24-31 nt piRNA

The smaller sizes could be the result of over-trimming, the mRNA byproducts as first mentioned, and/or minor degradation of your small reads. If the distribution of your read lengths (i.e. molecule lengths) matches what has been previously observed in the literature I wouldn't worry too much.

Here is an example for Drosophila from this paper: smallRNA profile Dros

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