Hi Martin Thank-you for your help with readAligned. The quality scores are in the correct range now. Going back to my question on alignQuality I had a couple of days ago I found found that all of the values are NAs. They exist since I am still able to generate the quality scores matrix. I typed ?alignQuality and it doesn't appear I'm missing any parameters. > alignQuality(aln) class: NumericQuality quality: NA NA ... NA NA (4933275 total) q <- quality(alignQuality(aln)) > sum(is.na(q)) [1] 4933275
> Date: Wed, 5 Aug 2009 09:21:56 -0700 > From: [email protected] > To: [email protected] > CC: [email protected]; [email protected]; > [email protected] > Subject: Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores > from bowtie > > Hi Faud -- > > > get NAs in both cases. Let me know how I can help to trouble shoot this. > > NA's in alignQuality are present when the reads did not align; not all > of the values will be NA. see below for the issue with base quality scores. Fuad _________________________________________________________________ [[elided Hotmail spam]] [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
