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Old 08-18-2013, 08:24 PM   #5
pengchy
Senior Member
 
Location: China

Join Date: Feb 2009
Posts: 116
Default

There is a bug for sam_juncs script, which is 1 smaller than the output of bed_to_juncs script.
here is the example:
output of sam_juncs
Code:
Scaffold184317  456     11046   +
Scaffold184317  11239   21151   +
Scaffold184317  21385   29565   +
Scaffold184317  34619   60733   +
Scaffold184317  61209   68778   +
Scaffold184317  69066   75556   +
Scaffold184317  75631   84372   +
Scaffold184317  75631   102072  +
Scaffold184317  104376  112269  -
Scaffold184317  112465  115516  -
Scaffold184317  115669  115888  -
Scaffold184317  116034  116975  -
Scaffold184317  117130  117392  -
Scaffold184317  117631  123099  -
Scaffold184317  123260  134557  -
here is the output of bed_to_juncs
Code:
Scaffold184317  457     11046   +
Scaffold184317  11240   21151   +
Scaffold184317  21386   29565   +
Scaffold184317  34620   60733   +
Scaffold184317  61210   68778   +
Scaffold184317  69067   75556   +
Scaffold184317  75632   84372   +
Scaffold184317  75632   102072  +
Scaffold184317  104377  112269  -
Scaffold184317  112466  115516  -
Scaffold184317  115670  115888  -
Scaffold184317  116035  116975  -
Scaffold184317  117131  117392  -
Scaffold184317  117632  123099  -
Scaffold184317  123261  134557  -
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