You could use the adaptor clip with e.g. a custom poly-A 'adaptor'
its in FASTX-Toolkit for FASTQ data

best,
ido

On Jul 28, 2013, at 8:44 PM, Larry Simpson <larrys3...@gmail.com> wrote:

> 
> Hi
> 
> Is it possible to trim a variable number of a specific nucleotide from the 3' 
> ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may have 
> this ability but I do not know  how to create a custom inquiry.
> 
> Thanks in advance for any assistance.
> 
> Larry
> 
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