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Old 09-11-2010, 12:12 AM   #4
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

Originally Posted by sandhya View Post
Infact when I used Novoalign to read the fastq file, it summarised the file as 'Interpreting input files as Sanger FASTQ'. So it could be that the files are Sanger-generated. Please let me know if this is right.
'Sanger FastQ' refers to the encoding scheme for the quality scores in the file. There are a few different ways this can be done and Illumina have their own encoding scheme(s), so you're probably correct in thinking these don't come directly from an Illumina run. Having said that, I think the main sequence repositories convert all qualities to Sanger encoding so it could be an Illumina file which has passed through a repository.
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