Hi Rizwan,

yes, a specific pipeline is used for transcriptomic data analysis it depends upon whether you have microarray or RNA seq data?

If you share more detail of your gene expression platform then it might be more helpful.

You may need to check some related articles, or you may look for some specific articles whose analysis was done by the same company. It will help you move on step by step. If I am not wrong, the company already have done everything for you, but you are new with transcriptome data as I was. So, you may need to understand the presentation/interpretation style which starts from raw data>transcriptome profiling>DEGs>enrichment analysis (GO/KEGG/others)>PPI>key pathways etc.

Rinki Singh @ Ali Raza i have RNA seq data, and company sent me different files such as 1-- raw data, 2-unigene assembly 3-geneExpression Unigene, 4_Unigene_Anno Unigene, 5-Unigene_Structure, 6_DEG_Analysis

as i did transcriptome of two fruit varieties at different developmental stages, ripening, harvesting, and now i am looking for their different gene expression profile for comparison

Muhammad Amjad Nawaz Thanks a lot of your sir,

I will have a look and will follow,

if there will be any further question then i will contact you,

Thanks again