what is the best practice to deal with the unpaired data generated by trimming paired-end RNA-Seq data, when only one of the mates makes it through the trimming?
I have seen people recommend to only use the paired data remaining (and ignore the often small unpaired files), but I am afraid to lose crucial data. I could easily process the paired and two unpaired sets per sample separatly
My analysis pipeline is
fastqc - trimmomatic - fastqc - STAR - featureCounts - voom/limma
If trying to use all data, at what point would you recommend to put everything together (and how)?