i have NGS data of microRNA at different time with 0 hour as control. the library construction and data analysis was done by a company. i want to know how to normalize the data?
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:
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:
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...
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