$re = '/^([^.]+)\_([^.]+)\_([^.]+)\_([^.]+)\_([^.]+)\.fastq$/m';
$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';
$subst = "$1_$4.fastq";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
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 PHP, please visit: http://php.net/manual/en/ref.pcre.php