Thanks for a quick revert. Kind of an expected question, when you talk
about quality format,  by default is it the Phred one ?  I will be
importing the FASTQ from Illumina Eland output which is 0-40 scoring
window.  Does that gets automatically converted ?

 

Thanks,

-Abhi

 

From: johannes.waage@gmail.com [mailto:johannes.waage@gmail.com] On
Behalf Of Johannes Waage
Sent: Monday, August 03, 2009 4:04 PM
To: Pratap, Abhishek; Bioc-sig-sequencing@r-project.org
Subject: Re: [Bioc-sig-seq] Calculating/plotting Avg Base Quality

 

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
<APratap@som.umaryland.edu> 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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