whether should keep same number of mate reads as input into Tophat

[canhu]

Hello all,

I use fastx-toolkit to fliter low quality reads from paired-end reads files respectively, which will lead to the different amount of reads in two files.
for a simple example,
i have tow files containing PE reads, read_1.fq and read_2.fq
read_1.fq have 5 reads,
A_1
B_1
C_1
D_1
E_1

also, read_2.fq have the same number of read
A_2
B_2
C_2
D_2
E_2

after fastx-toolkit fliter,
read_fliter_1
A_1
B_1
C_1
D_1

read E_1 was flitered out because of low quality in read_1 file.

read_filter_2
A_2
B_2
C_2
E_2

read D_2 was flitered out because of low quality in read_2 file.

when i use read_fliter_1 and read_fliter_2 as input into tophat, should i remove the read D and E ?