Hi, 

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
When a trimming program trims data one of the reads (assuming you are using paired-end data) may become short and fail a criteria you have set (e.g. minimum length 25 bp). At the point that read is removed by the trimming program. Let us say that was from R2 file. A trimming program should remove the corresponding R1 read from R1-file (even though that may have passed) when R2 read is dropped. If it does not do that you are left with an unpaired read in R1 file.<br><br>Aligners expect reads to be in the same order in R1/R2 files. If they are not then you can get strange results (e.g. discordant mapping). Presence of unpaired reads in main sequence files (As @mastal points out trimmomatic should collect them in separate files) generally signifies improper use of a trimming program (or using a trimmer that is not paired-end aware). If that happens `repair.sh` tool from BBMap suite can be used to remove those unpaired reads and bring R1/R2 files back in sync.