Confusion With Illumina Version And Phred Scores
1
0
Entering edit mode
12.2 years ago
Pasta ★ 1.3k

Hi there,

I received some old Illumina datasets to analyse that were generated using "GAPipeline-1.5.1" (that's what I read on the report file...). From what I guessed it means the quality scores are "Illumina 1.5 encoded", ie Sanger-type. Am I right ?

Sorry if the question sounds a but dumb ....

illumina next-gen sequencing quality • 8.3k views
ADD COMMENT
1
Entering edit mode
12.2 years ago
SES 8.6k

Illumina 1.5+ data does not use Sanger encoding (Phred+33). Have a look here for a description. If you are unsure about the encoding, FastQC will tell you which encoding you have (there may be other/better methods). If you need to convert your data to Sanger encoding, I recommend using the seqret tool from EMBOSS as it is faster than the BioPerl/BioPython methods in my experience.

ADD COMMENT
0
Entering edit mode

Thanks mate ;-)

ADD REPLY

Login before adding your answer.

Traffic: 2119 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6