Illumina 1.3 v 1.8 quality scores

[Graham Etherington]

Hi,
Is there/should there be any difference in the quality score format between Illumina 1.3 reads an Illumina 1.8 reads?
Many thanks,
Graham

[kmcarr]

If you mean the format with which Illumina encodes the quality score in their FASTQ files then no, there is no difference. All versions of the Illumina base calling software since pipeline 1.3 (both RTA and OLB) use the ASCII(Phred+64) encoding scheme.

There are however differences in the range of Q-scores you will see in the Illumina output. Check the FASTQ article on Wikipedia and you will see that they made a change at 1.5. It also seems that they made a change in going from 1.6 to 1.8. In 1.6 the maximum Q-score assigned appeared to be 34. Now in 1.8 it is 40.