Entering edit mode
Flores Torres, Mariana
▴
10
@flores-torres-mariana-6100
Last seen 10.3 years ago
Hello,
I wondered if anyone has experience with microRNA seq data analysis??
I have miRNA sequencing data from Illumina (control vs treatment) and
have used mirdeep2 for analysis (it uses bowtie to aligne to miRBase)
but I'm not sure how to perform differential expression, hope someone
could please guide me through this!
Many thanks!
Mariana
[[alternative HTML version deleted]]
hi mariana
i also have to do differential expression for mirna data
i have also used mirdeep2 tool for analysis
could u help me with edger
i have data as follows 2 conditions control vs treated
environment of two genotypes of wheat
i have biological replicates for each sample
my data is as follows:
i have counts of all my libraries in each condition ready with me as txt files
You should probably post a new question instead of adding to a comment to this question (which is almost 4 years old, now).
Before doing that, though, take note of Ryan's answer. You'd do well do try one of the rnaseq analysis toolkits (edgeR or DESeq2) on your miRNA data. I imagine you have a count matrix of miRNAs in rows and samples in columns.
Read through vignettes and user guide's to both packages. Once you have done that, use one of the workflows described there to do your analysis. If you decide to follow up with a new question, please be very specific about what you tried and the steps that are confusing to you so that you can get the best help.