Seeking Advice on Validating RNA-Seq Data Before Differential Analysis

Question

[Tully]

Hello, I recently received the RNA-Seq analysis results for a set of samples from a sequencing company. My plan involves the following steps:

1. Perform differential gene expression analysis to obtain a list of differentially expressed genes.
2. Utilize Gene Ontology analysis to determine the functional distribution of the differentially expressed genes.
3. Conduct KEGG pathway analysis to understand whether the differentially expressed genes are concentrated in specific biological pathways.
4. Integrate the results from GO and KEGG analyses to identify target genes.
5. Validate the findings through experimental techniques such as qPCR.

My question is, should I validate the reliability of the transcriptome data provided by the sequencing company before proceeding with these five steps? Your insights and experiences would be greatly appreciated!

[ATpoint]

Define 'validate'. Should you do a quality control towards the sequencing data itself (fastqc) and some checks towards sample clustering and presence of batch effects? Yes, absolutely. You should always check any data before any analysis.