Hi Rahul,

This is the maximum number of bases which can have their score not included when calculating the result of the selected aggregation function. 

For example, if you had a 5 base window with scores of 5,5,2,5 and 5, set aggregation to min score with a specified value of 4, with the action of ">=": 
0, for maximum number of bases to exclude, would trim
1, for maximum number of bases to exclude, would not trim

Thanks for using Galaxy,


On Nov 23, 2011, at 11:27 PM, Rahul Kanwar wrote:


  I am running Galaxy locally and it has been performing flawlessly! I wanted to get more insight about this flag in the FASTQ Quality Trimmer program:

Maximum number of bases to exclude from the window during aggregation

  Does it mean the number of 5' bases to exclude while the doing the trimming step [i.e. the sliding window starts this many bp after the read start] ? I would really appreciate if someone could shed more light on this. Thanks.


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