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How to use Rfam annotate small RNA and how to see differential expression of novel miRNA produced by mirdeep2?

Hello everyone

I am analyzing small RNA data currently, but there are some questions about Rfam and mirdeep result? could someone give me some advice, thanks!

  1. I use bowtie to map my reads to Rfam data to annotate the other ncRNA except miRNA, but the Rfam data including ncRNA from many species, I don't know just map my reads to the whole Rfam database or just the data of the species I study?
  2. I use mirdeep2 to predict the novel miRNA of each sample, but I want to do the differential expression of novel miRNA between different samples, but the name of novel miRNA given by mirdeep are really different, I don't know how to deal with it.
mirna rfam mirdeep
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updated by kuttibiotech2009 • kuttibiotech2009 • written by zm20074970 • zm20074970

1 answer

I guess I can shed some light on your second question. As far as I'm aware (although it's been about a year since I've used miRDeep2), there's no way to do novel miRNA differential expression. miRDeep2 works on individual samples, not whole experiments, but I do agree it'd be a useful thing!

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updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

Thank you for your reply, I found that there were about 1/3 same novel precursors between two samples in my data by using bedtools, but it's difficult to compare more than 2 samples

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updated by Ram Ram • written by zm20074970 • zm20074970

I am very glad that you are in Newcastle, I graduated from Newcastle University O(∩_∩)O~~

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updated by Ram Ram • written by zm20074970 • zm20074970

I am also facing the same issues. Can you please tell me how to do this using bedtools?

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written by kuttibiotech2009 • kuttibiotech2009

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