I use trimmomatic softwre for trimming and Iget 4output paired files(forward and reverse) unpaired (forward and reverse)
i didn't inderstand the diffirence between the paired and unpaired files
can you help me to inderstand please
Paired files contain reads that survive trimming and are retained in both R1/R2 files. When one of the reads is discarded from R1/R2 its mate is put in "unpaired" file. Doing so keeps the order of surviving reads in paired files intact.