Convert Illumina 1.5 to Illumina 1.8

Question

[thjnant]

Hello,

I have paired end RNA-seq fastq files that has the quality score of the earlier version of Illumina, such as Illumina 1.5. I need to convert their quality scores to the one of Illumina 1.8.

I was wondering if there is any script available for this purpose before I start on it myself.

Thanks,

[thjnant]

I found this solution:

sed -e '4~4y/@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghi/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJ/' myfile.fastq   # add -i to save the result to the same input file

[SES]

This can be done with standard tools, e.g. EMBOSS (the program 'seqret'), BioPython, or BioPerl. Check the "similar posts" to the right, or search "illumina to sanger" and you will find many solutions. Personally, I would just use a standard tool since they all agree.

Answer 1

[Docroberson]

Illumina 1.5 should be in Phred format. Do you mean you have older Illumina data in the +64 scale?

If you need to convert Illumina +64 to Phred +33 you can use a tool we have on GitHub.

Exercise caution, however, and make sure what offset you have. +33 is fine. +64 can be converted. The even-older Illumina format uses log-odds, and is not the same conversion. The FastQ wiki article may help you sort all this out. And I believe FastQC reports the quality scale when you run it anyway.