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Old 01-11-2012, 11:57 PM   #2
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
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Using Biopieces you can use plot_distribution like this:

Code:
read_fasta -i contigs.fna | plot_distribution -k SEQ_LEN -x


                                  Distribution
      +          +          +          +           +          +          +
  14 ++*---------+----------+----------+-----------+----------+----------+-++
      |*                                                                   |
  12 ++*                                                                   ++
      |*                                                                   |
      |*                                                                   |
  10 ++*                                                                   ++
      |*                                                                   |
   8 ++*                                                                   ++
      |** *                                                                |
   6 ++****                                                                ++
      |****                                                                |
   4 ++*******                                                             ++
      |*******                                                             |
      |***********       * *                                               |
   2 ++**********************                                              ++
      |******************************************* **  * *            *    *
   0 ++*******************************************-**--*-*----+-------*--+-*+
      +          +          +          +           +          +          +
      0        10000      20000      30000       40000      50000      60000
                                     SEQ_LEN

It is also possible to output to X11 terminal or PNG, PDF, PS, and SVG.

Installing Biopieces requires a working setup of Perl w. relevant modules and Ruby w. relevant gems. However, it should be worth the trouble since Biopieces is a nice toolbox IMHO.
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