Dear Bastian, May be a dull question. I am trying to use fastqselect.tcl to extract a subset of solexa sequences from a large fastq file. With the -name argument I provide a list of desired sequences in a file formatted as follows: HWUSI-EAS1676_0036_FC:6:1:14746:1149#0 HWUSI-EAS1676_0036_FC:6:1:16832:1231#0 HWUSI-EAS1676_0036_FC:6:1:19227:1242#0 HWUSI-EAS1676_0036_FC:6:1:16967:1346#0 HWUSI-EAS1676_0036_FC:6:1:17950:1378#0 HWUSI-EAS1676_0036_FC:6:1:5726:1395#0 HWUSI-EAS1676_0036_FC:6:1:3291:1663#0 HWUSI-EAS1676_0036_FC:6:1:19135:2061#0 HWUSI-EAS1676_0036_FC:6:1:18964:2200#0 HWUSI-EAS1676_0036_FC:6:1:1511:2675#0 HWUSI-EAS1676_0036_FC:6:1:19425:2835#0 ..... The script takes some time to produce an output file. But this output file is empty, although the input file does contain the sequences I am looking for. Could you tell me please what I am doing wrong Thank you Vladimir. -- Vladimir Mashanov, PhD Universidad de Puerto Rico Faculdad de Ciencias Naturales Departamento de Biologia JGD Building, #220 PO Box 70377, UPR Station Rio Piedras, PR 00936-8377 email: mashanovvlad@xxxxxxxxxxxxxx; Skype: vladimirmashanov