>Base quality by position

>A colleague of mine was working on a nifty tool to give graphs of the base quality at each position in a read using Eland Export files, which could be incorporated into his pipeline. Over a discussion about the length of time it should take to do that analysis, (His script was taking an hour, and I said it should take about a minute to analyze 8M illumina reads…) I ended up saying I’d write my own version to do the analysis, just to show how quickly it could be done.

Well, I was wrong about it taking about a minute. It turns out that the file has a lot more than about double the originally quoted 8 million reads (QC, no match and multi match reads were not previously filtered), and the whole file was bzipped, which adds to the processing time.

Fortunately, I didn’t have to add bzip support in to the reader, as tcezard (Tim) had already added in a cool “PIPE” option for piping in whatever data format I want in to applications of the Vancouver Short Read Analysis Package, thus, I was able to do the following:

time bzcat /archive/solexa1_4/analysis2/HS1406/42E6FAAXX_7/42E6FAAXX_7_2_export.txt.bz2 | java6 src/projects/maq_utilities/QualityReport -input PIPE -output /projects/afejes/temp -aligner elandext

Quite a neat use of piping, really.

Anyhow, the fun part is that this was that the library was a 100-mer illumina run, and it makes a pretty picture. Slapping the output into openoffice yields the following graph:

I didn’t realize quality dropped so dramatically at 100bp – although I remember when qualities looked like that for 32bp reads…

Anyhow, I’ll include this tool in Findpeaks 4.0.8 in case any one is interested in it. And for the record, this run took 10 minutes, of which about 4 were taken up by bzcat. Of the 16.7M reads in the file, only 1.5M were aligned, probably due to the poor quality out beyond 60-70bp.

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