I think you are best off finding a way to work on Linux. Either install Linux as dual-boot (on a separate hard drive partition), or on a virtual machine.

I think you are best off finding a way to work on Linux. Either install Linux as dual-boot (on a separate hard drive partition), or on a virtual machine.

I agree with Tyler. Better start using Linux. It has all freely available softwares for NGS analysis. Windows based pipelines are all commercial

Hello,

I definitely agree that the best solution is to find/install linux computer, but have you tried Galaxy? https://usegalaxy.org/

It should be platform independent, you can give it a chance.

Good luck,

Silvia

Well, If you really wanna go with windows then try Galaxy. But I would strongly suggest to carry on your analyses on Linux based platform. 

I can give a look at BRB-SeqTools at the link bolow.

However, this is only for RNA-Seq.

https://brb.nci.nih.gov/BRB-ArrayTools/

Why not R? It's free and runs on Windows, Linux or MacOS.

https://www.r-project.org

https://www.bioconductor.org/packages/release/BiocViews.html#___Sequencing

I suggest using PubMed to search for some of the excellent, recent tutorials from Simon Anders and Gordon Smyth on the use of edgeR and DESeq.  Even if you don't choose to use these specific packages in your analyses, I think it's possible to glean a good deal of essential R code and commands, without needing to study many extra tutorials.  Articles of this kind were invaluable to me as I learned to use R for the first time for NGS work. 

Some thing you can do it in ugene

http://ugene.net/en/

Linus is a possibility as suggested but anyway you will end up in the same situation. I have good experience with CLC Genomics.

CLC program has a lot of options and you need to know what they are.

My suggestion:

1)summarize your scope...

2)what type of analysis

3)your experience

 before getting anything.

 Before buy anything is important to get some experience in data analysis. Get in contact with researcher close to you and see what they use and how they do it.

Good luck

 Roberto

Galaxy is a good option, however unless you run a local copy of Galaxy, you will have to upload your fastq or other NGS files to the Galaxy server, which may be tedious if you have a lot of samples.

I would still recommend Linux but since your question clearly implies Windows I would highly recommend to use R/Bioconductor. As suggested above you can use Galaxy. Also, I would say you should check this link-

https://bow.codeplex.com/

and see if there are tools which you can use.

Hope it helps.

Try SeqMonk. Especially for RNASeq it is perfect. Easy to use. Multiple statistical methods. User friendly. You can find how to use videos from youtube.

I would also suggest GALAXY for NGS data analysis.

https://usegalaxy.org/

Galaxy, SeqMonk and UGENE are all good for NGS analysis, although CLC genomics is the best if you can afford it.

I can recommend SeqMonk if you focus on CHIPseq or RNAseq. It has a lot of 'easy to use' methods and a nice YouTube introduction.

The last version I used had problems with multiple transcript isoforms and CLIP data. So I wouldn't use it for alternative splicing analysis e.g.

I would recommend galaxy (https://usegalaxy.org/). It is is an open source, web-based platform for NGS data analysis which includes RNAseQ, DNA sequencing data and SNP calling etc. It integrates several widely used tools for NGS data analysis using which you can develop your own pipeline for analysis. All you need is to create a login on its web interface.

All the best.

I recommend Varstation (http://www.varstation.com). It is a cloud-based platform and performs end-to-end genetic files processing (mapping and variant calling) as well as variant annotation and classification. The tool already contains validated pipelines by bioinformatics specialists.

Try

BTW—Bioinformatics Through Windows (https://github.com/vpylro/BTW)

It allow you to use linux based analysis on windows itself

Basepairtech.com has a free two-week trial. Not permanently free, but you can run unlimited analyses on six samples.

It's cloud-based and the pipelines are automated so non-bioinformatics people can use it.

You surely mean basepairtech.com

You can use CSI NGS Portal for free online NGS data analysis without sign up/login requirement !

https://www.preprints.org/manuscript/201910.0146/v1