Try this:
library(ShortRead)
my_reads<- readFastq("~/", pattern="my_reads.fastq")
qualities <- FastqQuality(quality(my_reads))
qualities <- as(qualities, "matrix")
boxplot(as.data.frame((qualities )), outline = F, xlab="Cycle",
ylab="Quality")
Depending on quality format, you might have to correct your numeric values
in the matrix, or even convert to base call probabilities.
Regards,
Johannes Waage,
Uni of copenhagen
On Mon, Aug 3, 2009 at 9:41 PM, Pratap, Abhishek
<[email protected]>wrote:
> Hi All
>
>
>
> Just wondering if there is a R function in any package to do the
> following. Want to make sure before I write something.
>
>
>
> We would like to calculate avg base quality score for each base called
> per cycle / lane. What will be nice is to also plot these avg quality
> scores/lane for couple of different runs.
>
>
>
> Thanks,
>
> -Abhi
>
>
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>
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