Fastq Illumina 1.8+ And Sanger

Question

[arkarachai.af]

I wonder whether we need to modify fastq from Illumina1.8+ to make it as Sanger fastq. Even though fastq from Illumina 1.8+ is said to be the same as Sanger fastq, the quality score range is not precisely the same (0-41 for Illumina1.8+ and 0-40 for Sanger fastq) Anyone know whether we can just treat fastq from Illumina 1.8+ as Sanger fastq?

Answer 1

[Devon Ryan]

Just treat them the same, you don't need to rescale or anything. It's possible that some old scripts could error out (perhaps they have a hard-coded maximum value), but I've never run into such a case.

Answer 2

[Drei]

If you wanted to be extra safe, you could always use a simple script to replace any values of 41 to 40. It's extremely likely you won't have any issues, but if you have a pipeline using a whole bunch of various bioinformatics tools, it can pay to be paranoid.