I am a new PhD student, started this month and got to analyse the RNA-Seq data. I have no knowledge regarding this. I have no idea what to do and how. I have a few Excel files with thousands genes data in it. what i guess is this data is already been analysed and now I have to sort this data into most significant up and down regulated genes with a proof that these are true significant genes by comparing then with control group genes.
We'll need a lot more information to help, you haven't given us much to work with.
What organism are you working in?
What is the experiment e.g., sample types, treatments/conditions? What is the hypothesis/question you are trying to answer?
Can you at least proved a snippet of the data you have so we can see the column headers?
I think the situation you are finding yourself in is quite common. On a general note, as you are at the beginning of your PhD program, you can and should afford some time to learn the basics. You will also have to take some courses as part of your curriculum. Try to choose courses on Genomics and data analysis. Talk to your supervisor to agree on the courses from your graduate program you should take.
Another way is through self-study. For this purpose, the book "RNA-seq by example" from the Biostars handbook series will be a good start.
Finland, like most European countries, is part of Elixir. Elixir organizes courses covering various topics within genomics and data management. You are entitled to sign up for these courses and they can be found via TeSS. Elixir Norway is running a boinformatics help-desk (for which researchers like me are working), possibly Elixir Finland has something similar, too. They could be able to provide more specific or local help.
Online course: ANALYSIS OF RNA SEQUENCING DATA WITH R/BIOCONDUCTOR
Dates 4-15 November 2024