I was reading this paper from 2010 : https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-94#Sec11
It is mentioned that
One inherent bias of the illumina platform is the preferential sequencing of longer genes. Hence, longer genes are more likely declared as DE.
Is it true for the current Illumina platforms as well? And as a result, we observe low counts for some of the genes. For example, I am looking at the gene PYCR1, and after performing DEseq2 I have got good Log2foldchange (3.63) and Padj-value (1.95E-06), however, the basemean is about 23. Now, it is a known fact that in cancer this gene is upregulated, but the counts are not convincing. I am really confused about what to do here!