How can I do normalization of miRNA seq illumina data?

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Simonas Juzenas Popular answer

You can use Bioconductor's DESeq2 or edgeR packages. These packages are very well documented and commonly used for RNA-seq normalization. You will find the information in the following links below:

http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html

http://www.bioconductor.org/packages/release/bioc/html/edgeR.html

Simonas Juzenas

Najib Abdellaoui

thanks a lot for your help. the problem i never used R before and which input data i should use?

Delphine Fagegaltier

We provide details and pointers on normalization methods in the article below. Try several methods of normalization and perform validation using independent methods (e.g. qPCR).

Best of luck!

Article A Genome-Wide Survey of Sexually Dimorphic Expression of Dro...

Jan Oppelt

You can also have a look on these two articles. I recommend you look at both since the second one is a reaction of one of the normalization methods authors discussed in the first one.

Personally, I use edgeR normalization. I tried to compare it with DESeq2 normalization and it looks almost the same on my set of microRNA data. You are fine even if you never worked with R. If you take a look into links Simonas sent and look for a user guide/vignette you can (almost) just copy and paste the commands and get the normalized results.

The other question is what you want to do with the data next...

Article Evaluation of normalization methods in mammalian microRNA-Seq data

Article MiRNA-Seq normalization comparisons need improvement

thanks a lot for your help. our study is the study the effect of virus infection on microrna expression in cell culture depending on time. so the next step after getting the deferentially expressed microrna is to confirm it by real time PCR. thanks for your kind answer.