I am very new to RNA-seq data analysis and Galaxy platform. I tried to analyze an SRA data through Galaxy using trinity. However, there are questions regarding the analysis in my mind.
1-After running fastqc, I cannot find trimmomatic tool on the Galaxy.
Do I have to run fastqc in de novo approach?
If yes, Which tool can be used instead of trimmomatic?
2-After reference genome was downloaded and Trinity was run.
Do I need to asses quality of assembly? Assemlystats tool is not available on the Galaxy.
If yes, Which tool should be used for that ?
3- Blastn was used for annotation. Later Salmon was employed for quantification and TPM values were obtained.
How can I get fold changed values for each condition for each gene? Tool name?
How can I find DEGs?Steps ? Tool name(s)?
To make a long story short, is there anyone who can provide me an up-to-date documentation articulating each step in RNA sequencing De Novo Assembly in detail?