Quality trimming in R using ShortRead and Biostrings

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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.
#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
function(x){which(x < minQuality)[1]-1}))
#length=end-start+1, so set start to no more than length+1 to avoid negative-length
#use whatever QualityScore subclass is sent

#apply minLength using srFilter
lengthCutoff <- srFilter(function(x) {
},name="length cutoff")

To use:
source("softTrimFunction.R") #or whatever you want to name this
reads<-readFastq("myreads.fq") trimmedReads<-softTrim(reads=reads,minQuality=5,firstBase=4,minLength=3) writeFastq(trimmedReads,file="trimmed.fq") 
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

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