miRNA length distribution
Hi all
I'm working with small RNA-seq data and my aim is to look at miRNA DE.
I trimmed apadters using bbmap. But it didn't remove all the adapters (because one of them was not in adapters.fa). The remaining adapter was found with fastqc and then I removed it with cutadpat. In original files read length was up to 50 nt, so I filtered out reads shorter than 19 nt and longer than 26.
And there is the issue. The peak length is 24 nt. Is it ok? Shouldn't it be 21-22 nt? Or do I just have a lot of other small RNAs and there is nothing to worry about?
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LynxLynx •
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With miRNA you need to be cautious since kits may use a specific adapter and/or have instructions on how to post-process.
That said you could have simply provided the adapter sequence you wanted eliminated on command line to
bbduk.shasliteral=seq1,seq2 ..or it could have been simply added to end ofadapters.fafile.miRNA are about that size so it sounds ok.
Thank you!