bp_usage/read_solexa

   1 Author:         Martin Asser Hansen - Copyright (C) - All rights reserved
   2
   3 Contact:        mail@maasha.dk
   4
   5 Date:           April 2008
   6
   7 License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
   8
   9 Description:    Read Solexa deep sequenceing output files. Lowercase sequence indicates low quality.
  10
  11 Usage:          $script [options] -i <Solexa file(s)>
  12
  13 Options:   [-i <file(s)> | --data_in=<file(s)>]  -  Comma separated list of files or glob expression to read.
  14 Options:   [-n <int>     | --num=<int>]          -  Limit number of records to read.
  15 Options:   [-q <int>     | --quality=<int>]      -  Lowercase nucleotide with quality score below this limit (min:0 max:40)  -  Default=20
  16 Options:   [-I <file>    | --stream_in=<file>]   -  Read input stream from file                                              -  Default=STDIN
  17 Options:   [-O <file>    | --stream_out=<file>]  -  Write output stream to file                                              -  Default=STDOUT
  18
  19 Examples:   $script -i test.solexa             -  Read Solexa entries from file.
  20 Examples:   $script -i test1.fna,test2.solexa  -  Read Solexa entries from files.
  21 Examples:   $script -i '*.solexa'              -  Read Solexa entries from files.
  22 Examples:   $script -i test.solexa -n 10       -  Read first 10 Solexa entries from file.
  23 Examples:   $script -i test.solexa -q 10       -  Change quality score threshold to 10.
  24
  25 Keys out: SEQ_NAME    -  Name of sequence.
  26 Keys out: SEQ         -  Sequence.
  27 Keys out: SEQ_LEN     -  Length of sequence.
  28 Keys out: SCORE_MEAN  -  Mean quality score.