These classic papers may help you a lot.

Article RNA Sequencing and Analysis

Article A Survey of Best Practices for RNA-seq Data Analysis

http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

R environment is to my experience the best.

Other possibilities are commercial softwares.

Can you give some specifics about what kind of analysis you want to do (eg. differential expression, alternative splicing, fusion discovery, etc.) and what organism you're working with? This will help you get more specific feedback on software and tutorials to help you.

Cameron J Grisdale i had done Transcriptome by Company ( two fruit varieties peel as samples with three replications , yellow and purple) , now i have Raw material so i would like do analysis about the color related genes, there pathways, and expression, so its my first time to do transcriptome analysis so i would like you to help

Do you have also genome sequence? annotation?

Basically you are interested in differential gene expression analysis and screen for the cluster involved in color pathway, right?

Loubna Youssar yes i have annotation data given by company , yes i am interested in differential gene expression analysis and screen for the cluster involved in color pathway,

so i have no experience that how to start and how to do analysis, and which pathways should select, and which software will be needed, as i have read different articles, but everyone used different software and different way of analysis

As I suggested you before, if you have any programming skills, R is your friend. Otherwise its easy to learn and the language most used for omcics/statistics. Start first by installing R and Bioconductor: https://www.bioconductor.org/

Then you will have to download many packages and they is somewhere a "default" workflow you have to follow the instructions.

A quick google shows me a free course: https://www.datacamp.com/courses/rna-seq-differential-expression-analysis

The second option is to use Galaxy (platform for biologists). Its for free, you have only to register to any institution they have an instance. I guess an account in galaxy Europe should be easy to get

https://usegalaxy.eu/

Use this training tutorials, very helpful:

https://training.galaxyproject.org/

Best

I agree with the suggestions from Loubna. You should get familiar with working in R and Bioconductor to do DE analysis, or if you have no command line experience and want to avoid it you could use Galaxy.

If you have sequencing reads, you need to preprocess your data (e.g. sequence alignment using tophat, bowtie, bwa etc). If the company gave you raw data, you can use edgeR in bioconductor (https://www.bioconductor.org/ ) to identify DEGs. Compared to DESeq2, edgeR usually gives better number of DEGs that enable you do further analyses.

Saurabh Mandal Thanks sir for sharing ,

Hairong Wei Thanks sir