I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff, star+stringtie+cuffdiff etc. However, among all the pipelines, only the Cuffdiff differential tool gave some gene with significant Q value whereas none others gave DEGs with significant adjusted P-value. So I would like to know from the people who are working with brain samples, what possible ways can be used for analyzing such data? What kind of adjusted P-value and log2fold change do you observe in your routine analysis?? Is there any specific normalization technique or pipeline for analyzing brain tissue samples??