fastq Groomer action

Question

[daffodil]

Hello every body

Actually I am starting to learn analysis of NGS data, I apologize of my simple question. I wonder why we have to convert Illumina reads To Sanger score? Please let me know about the action of fastq groomer.

Answer 1

[h.mon]

You do not necessarilly have to convert old Illumina files to Sanger score, you have to convert only IF the software to be used accepts only Sanger score. To understand Phred score on fastq files, see the FASTQ format wikipedia page - look at the "Encoding" section.

Answer 2

[GenoMax]

Q-scores in Sanger format have become the de facto standard for NGS data and most programs (aligners etc) expect the data to be in that format. So that is one reason you would want to convert the scores (if they are not in that format). If your data is of recent vintage then this conversion is not needed since the data is in the correct format.

Fastq groomer will convert data from other formats to Sanger fastq.