I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.

This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.

#softTrim
#trim first position lower than minQuality and all subsequent positions
#omit sequences that after trimming are shorter than minLength
#left trim to firstBase, (1 implies no left trim)
#input: ShortReadQ reads
#       integer minQuality
#       integer firstBase
#       integer minLength
#output: ShortReadQ trimmed reads
library("ShortRead")
softTrim

To use:

library("ShortRead")
source("softTrimFunction.R") #or whatever you want to name this
reads

I strongly recommend reading the excellent UC Riverside HT-Sequencing Wiki cookbook and tutorial if you wish to venture into using R for NGS handling. Among other things, it will explain how to perform casting if you have Solexa scaled (base 64) fastq files. The function should respect that. http://manuals.bioinformatics.ucr.edu/home/ht-seq