What is the most popular and best tools/pipeline for small RNA seq analysis?

Question

[FAST_GENOME]

Dear All

I have to analyze a small RNA-seq data. This is my first time working with small RNA. I search threads here but the most recent is 2013.There are several new tools/publictions since 2015 but they doesn't have much citations. I have no hint how to make choose. What is the most popular and best tools/pipeline for small RNA seq analysis?

Any help will be appreciated.

[GenoMax]

Some options here. small RNA-seq pipelines

Answer 1

[Prasad]

sRNAworkbench one of the easiest tool for the analysis. Apart from that

List of tools in OMIC tools, rna-seq, miranalyzer, shortran

Answer 2

[Floris Brenk]

https://oasis.dzne.de/ is a good one!

Answer 3

[igor]

Here a few options you can look into:

• miRge - http://atlas.pathology.jhu.edu/baras/miRge.html
• miRDeep2 - https://www.mdc-berlin.de/8551903/en/
• miRExpress - http://mirexpress.mbc.nctu.edu.tw/

Answer 4

[accfree]

Another option is the SPAR small RNA-seq analysis webserver: https://www.lisanwanglab.org/SPAR.

Code: https://bitbucket.org/account/user/wanglab-upenn/projects/SPAR

Paper: https://doi.org/10.1093/nar/gky330