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

Question

[zm20074970]

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.

Answer 1

[andrew.j.skelton73]

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!

[zm20074970]

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

[zm20074970]

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

[kuttibiotech2009]

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