Hello. I would rather prefer to use Bioconductor. You need to install R and the bioconductor package, then follow the manuals of the specific packages you need. More specifically, the QuasR package is very easy to use and appropiate for RNA-seq, miRNA peofiling, methyl-seq and chip-seq. Using R might seem difficult at first, but once you are accostumed to it you can do it all inside it. Cheers!

Ok Adrián. I realize that R is very useful, but it is far to be "user friendly". In fact I have not too much time to learn R.

Then Galaxy is the best option. You can process your files and do DE tests in a user-friendly environment. Cheers.

following these nice discussion, What about genespring in analysing the deep seq data for miRNA profiling ? I have it here and wanted to use it

Any suggestions ?

@Mohamed-.... I agree with Rohan. Very nice and fancy tool, and very expensive too.

have you tried miRDeep:

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

http://www.nature.com/nbt/journal/v26/n4/abs/nbt1394.html

You have also ncPRO-seq to annotate miR in smallRNA-seq.

Website : https://ncpro.curie.fr/

Download : http://sourceforge.net/projects/ncproseq/

There will be a galaxy-based web service in a couple of weeks for exactly this issue. Although it's not locally installed, you can transfer compressed files via ftp. Feel free to contact me, if you wish to get preliminary access or more information!

if you have any knowledge about linux enviroment, I would recommend you analizing it that way. If you look on the seqanswers web page you could find information about how to analize your data. In any case these option is not very friendly.

As Mohamed and Rohan said Genespring is an expensive option but in my opinion it is limited to a specific pipeline...

Also, it exists Partek Genomics software which can handle this kind of data (although it is expensive you could download a full demo version if you contact them) but has the same problem as GS.

Have you tried srna-workbench..?

It features optimized pre calculated parameters for both plant and animals (can also be customized). It also provides the quantification and differential analysis results. Precursor and mature binding image can also be generated from the tool.

tool can be downloaded from the below link: http://srna-workbench.cmp.uea.ac.uk/

Check out http://www.nature.com/natureevents/science/events/47533-microRNA_Analysis_Using_Next_Generation_Sequencing