Hi Abhi, That depends on the version of the pipeline, and post-processing. I would suggest that you check the final qualities matrix before plotting, and see how the min and max turn out. Adjust the matrix to fit the 0-40 window, optionally convert to called/miscalled probabilities, and plot.
Regards, Johannes On Mon, Aug 3, 2009 at 10:22 PM, Pratap, Abhishek <[email protected] > wrote: > 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
