I am a beginner of the RNA seq. Now I do some analysis about the paired-end data. For filtering the raw data, I use the Trimmomatic to classify the data to two parts: unpaired reads and paired reads.
So, I don't understand what's the unpaired. Because every reads should have its partner, I always get the same number of the Reads 1 and Reads 2. Why exist the unpaired reads?
Thanks for your reply. Yunlong