I have stranded, paired end RNASeq reads that I have aligned using STAR. I plan do conduct a differential expression analysis with DESeq2. After running quality control checks, a good portion of my reads are aligned but I'm a little concerned about the proportion of properly paired reads
Here is the inner distance plot for the samples
For human RNA sequencing, does anyone have a rule of thumb that they'd consider is an appropriate proportion of properly paired reads? Are there any good papers that talk about this issue? As MultiQC marks the column as yellow, I'm concerned the proper pair percentage may not be satisfactory.
How important are properly paired reads for differential expression analyses?