microRNA analysis (no reference genome)

[emmecola]

Hi everyone

We performed an RNA-seq experiment using small RNAs in a species with no genome sequence. I've used miRProf to find which microRNAs are expressed in a control sample (3 replicates) and in a stressed sample (3 replicates).

Now I would like to calculate the Fold Change between the two conditions, but I have no idea about the expected inter-replicates variability. Which criteria should I use to filter out expression values with too much difference between the replicates?

Thanks
Moreno

[NicoBxl]

you can use DESes or edgeR , R packages.

There are part of the bioconductor package