Hi, Bastien The command line was: fastqselect.tcl -infile Illumina.fastq -name seqs.names -outfile seqs.fastq The input file: @HWUSI-EAS1676_0036_FC:6:1:10274:1044#0/1 CACAGACAAATTACTCAGCCTCATTATAAATTAAAGGC +HWUSI-EAS1676_0036_FC:6:1:10274:1044#0/1 gggggggggfggfggggaggggggdeggfgg_fffffd @HWUSI-EAS1676_0036_FC:6:1:2210:1056#0/1 TTTTTAAAAAAATCTTAAACCTTTTCTGAGGACTTCAGATTCATTAAGGTGATTAAC +HWUSI-EAS1676_0036_FC:6:1:2210:1056#0/1 hhhhgcffhehg`hhghgghchggeec`ggadahhhcddfdhdfffddaW_aabbb^ @HWUSI-EAS1676_0036_FC:6:1:2331:1055#0/1 GAAGACAGTTAAGAAAATACTTGGTAAGAAGACTACTAGGAG +HWUSI-EAS1676_0036_FC:6:1:2331:1055#0/1 _facefec]deffdfc\c``fcc[_`\`\\`cacbbdWaa]e @HWUSI-EAS1676_0036_FC:6:1:2844:1049#0/1 TTACGCTTGTGGAGTATAACATCACTCGTGAACGTCTG +HWUSI-EAS1676_0036_FC:6:1:2844:1049#0/1 eaddf_dfcbff]f]cX^Z^Y\Y``[bdbbbbce`a_d @HWUSI-EAS1676_0036_FC:6:1:4007:1055#0/1 ATTTGCACCTTACTTATCTTAGTAGGTCTTAATTAA +HWUSI-EAS1676_0036_FC:6:1:4007:1055#0/1 \cdaddfffff_fff_faccfdbadbb]ddaafffc @HWUSI-EAS1676_0036_FC:6:1:6070:1048#0/1 ATCCAGAGCACAAAGTTTTGTCTCAAGTTCTGCTCT +HWUSI-EAS1676_0036_FC:6:1:6070:1048#0/1 cccc_cZ\^aaccccc_aa^_cccccaccccccccc @HWUSI-EAS1676_0036_FC:6:1:6804:1059#0/1 TACCTCCATTAAGACGAAACCTGTAGAGTGCCATAGGATGTTGTGTACTACACATCGGTTA +HWUSI-EAS1676_0036_FC:6:1:6804:1059#0/1 ggfgggggggggfgdggggggggdggggcgaddbaagddgddgdcdc\_a_cddaca___a @HWUSI-EAS1676_0036_FC:6:1:7860:1049#0/1 GCAAAAGGGAGGAGAGGGTAAGAGGCTGTGCCCGC +HWUSI-EAS1676_0036_FC:6:1:7860:1049#0/1 _ffca]\_\T\XGZP`Z\[\U\YZX`b^b`[_P^^ @HWUSI-EAS1676_0036_FC:6:1:8218:1056#0/1 ATTTATTGAGCTTGCTTTAAAATTCCATCTTTAGTAACC +HWUSI-EAS1676_0036_FC:6:1:8218:1056#0/1 afffffg`gdggggdggggfaggggffgfgggggegggg On 29 October 2011 19:18, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > ** > > On Saturday 29 October 2011 22:16:18 vladimir mashanov wrote: > > > Could you tell me please what I am doing wrong > > > Not without seeing the data and the command line you used. Can you paste > the first, say, 20 lines of your FASTQ file and the command-line you are > using? > > > B. > > > -- 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