$re = '/((?:JQ1|mock)_(?:BRD4|input)_(?:A|B))/';
$str = 'DNA160630JA_JQ1_BRD4_A_S4_L001_R1_001.fastq
DNA160630JA_JQ1_BRD4_B_S8_L002_R1_001.fastq
DNA160630JA_JQ1_input_A_S3_L001_R1_001.fastq
DNA160630JA_JQ1_input_B_S7_L002_R1_001.fastq
DNA160630JA_mock_BRD4_A_S2_L001_R1_001.fastq
DNA160630JA_mock_BRD4_B_S6_L002_R1_001.fastq
DNA160630JA_mock_input_A_S1_L001_R1_001.fastq
DNA160630JA_mock_input_B_S5_L002_R1_001.fastq';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
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