I performed sortmeRNA using the following command:
sortmerna --ref ref_files --reads input.fq --aligned output_rRNA --other output_clean --log -a 12 -v --paired_in --fastx
After unmerging "clean", I got "cleanFV" and "cleanRV". I assume that FV and RV files should have the same number of lines since they are paired, but when I checked it using wc -l, they are of the different number of lines. However, FastQC showed the same number of reads for the two files, and the sum of FV, RV and rRNA read number equals to the total number of reads of my input file. Can anyone explain why I got different number of lines but the same number of reads?