Can ambiguous IUPAC nucleotides (R, S, Y, K...) ever appear in the raw reads from a fastq file?

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Gael Lecellier

Dear Xavier,

I can recommend these papers: Brief Bioinform. 2011 Sep; 12(5): 489–497.

Published online 2011 Jan 17. doi: 10.1093/bib/bbq077 and Biometrics. 2010 Sep; 66(3): 665–674.

doi: 10.1111/j.1541-0420.2009.01353.x

They explain why Phred scores, as opposed to IUPAC codes, are more widely used.

Xavier Bofill-De Ros

Thanks for your help Gael!

Mohamed Abdallah Turky

IUPAC nucleotide code :-

https://www.bioinformatics.org/sms/iupac.html
https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_nt_abbreviations.html