Quality Control and Quality Values

[agc]

As I understand it, each base in a read is given a quality value, and the higher the value the more likely the base read is accurate. I don't understand some things about the QV though -

1) How is it determined? What is it based on?
2) What is the range of values? What is considered 'good'?
3) I'm using ABi SOLiD - are the QVs based on colorspace? Should this make a difference to me?

I was also wondering about quality control. Should I be running something on my results to ensure that they are of good quality, or at the very least somehow sift out the lower quality reads?

Thanks.

[simonandrews]

The quality values are a transformation of a probability value that the base call is incorrect. They're generally some measure of the signal to noise ratio for that base call (ie how much better the signal was for the called base than the next best base).

The range of values goes from 0 to as high as you like (most machines have a practical limit of 30-40 for their highest quality value). The higher the quality the more likely the call is to be correct. Many people use a quality score of 20 as the threshold for a good call since this represents a 1% error rate.

Details of the conversion between p values and quality values are set out quite nicely in the wikipedia FastQ article.

Many mapping programs will use the quality values to bias their alignments so you may not need to remove poor quality reads. Some people do pre-filter their sequence data to remove reads with universally poor quality before doing any alignment though. For assembly you may find it more important to remove or trim reads with poor quality.

As a quick plug for one of our packages you can get a quick idea of the quality of a sequence dataset using FastQC

[drio]

This is useful too: http://maq.sourceforge.net/qual.shtml

[epigen]

Is there a quality controls tool similar to the fastx toolkit that can deal with ABI SOLiD color space data? Maybe I'm looking at all the wrong places but I couldn't find one.

[simonandrews]

FastQC can analyse colorspace fastq files, but it does the sequence analysis parts by converting to base calls which possibly isn't ideal. It may be enough for what you're trying to achieve though.