[BioC] shortread base quality

David martin vilanew at gmail.com
Fri Aug 24 16:09:45 CEST 2012

I'm trying to get the quality scores for each nucleotide for each read 
from the fastq file.
Here is how it starts. I know to get average scores for reads but not 
for each individual nucleotide of each read.

file <- "file.fastq"
fqfile <- paste(basename(file),"",sep="")
path <- dirname(file)
sp <- SolexaPath(path,dataPath=path,analysisPath=path)
fq <- readFastq(sp, fqfile)

#Get quality scores
score <- alphabetScore(fq)

#Gives the sum of the base quality scores for each read
aveScore <- score / width(fq)

#How can i get the score for each base for each read ????


More information about the Bioconductor mailing list