A
B
C
D
E
F
and file 2:
G
H
I
J
K
L
and get:
AG
BH
CI
DJ
EK
FL
Use awk like this (robbed and modified from various places on the internet):
awk '{str = $0 ; getline < "run1717_1731_1.end2.pf.fastq" ; print str $0 > "run1717_1731_1_joined.fastq"}' run1717_1731_1.end1.pf.fastq
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