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: [email protected] [mailto:[email protected]] On Behalf Of Johannes Waage Sent: Monday, August 03, 2009 4:04 PM To: Pratap, Abhishek; [email protected] 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 <[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 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
