Question: Question About Fastq Groomer
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Timothy Hughes • 20 wrote:
Hi Jianchao,
The different fastq formats are broadly summarised by:
S - Sanger Phred+33, 41 values (0, 40)
I - Illumina 1.3 Phred+64, 41 values (0, 40)
X - Solexa Solexa+64, 68 values (-5, 62)
However, at least in my version of the MAQ software (some months old),
sol2sanger conversion converts from X to S and NOT from I to X. So if
you feed I to the MAQ converter you are going to get slightly
incorrect Sanger qualities (because it is expecting the input
qualities to have been calculated using the Solexa formula but they
have in fact been calculated using Phred). If you search on
seqanswers.com you will find a post that details how you need to
modify the MAQ conversion script to make the conversion from I to S.
Could this explain the discrepancies you observe?
Tim.
--
Tim Hughes PhD (http://digitised.info)
Medical Genetics Department
Oslo University Hospital Ullevĺl
Kirkeveien 166
0407 Oslo
Norway