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,

Dan


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

> Hello,
> 
>   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.
> 
> regards,
> Rahul
> 
> 
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