use strict;
my $str = 'A10_S65_L001_R1_001.fastq
A8_S49_L001_R2_001.fastq
B7_S42_L001_R1_001.fastq
C5_S27_L001_R2_001.fastq
F4_S22_L001_R1_001.fastq
G2_S7_L001_R2_001.fastq
H1_S165_L001_R1_001.fastq
A10_S65_L001_R2_001.fastq
A9_S57_L001_R1_001.fastq
B7_S42_L001_R2_001.fastq
C6_S35_L001_R1_001.fastq
F4_S22_L001_R2_001.fastq
G3_S15_L001_R1_001.fastq
H1_S165_L001_R2_001.fastq';
my $regex = qr/^([^.]+)\_([^.]+)\_([^.]+)\_([^.]+)\_([^.]+)\.fastq$/mp;
my $subst = '$1_$4.fastq';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html