While analyzing #RNAseq data of D. mel salivary glands, we found that #Illumina #stranded protocol produces reads that are actually in both directions (not stranded) for low U content mRNA regions!
This was a nice journey digging into the reads
www.biorxiv.org/content/10.6...
biorxiv.org
The Illumina Stranded mRNA protocol is not strongly stranded for mRNA with low U content
The Illumina TruSeq Stranded and Illumina Stranded mRNA protocols are commonly used for strand-specific bulk RNA-seq and they typically yield >99% antisense reads. We show that these protocols can gen...