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Old 06-17-2011, 09:55 AM   #1
sunsnow86
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Default how to transfer sanger fastQ into illumina FastQ

I just got back my Hi-Seq data which use CASAVA 1.8 to process the data and the quality scores are now in Sanger format Does anyone know a script which can transfer sanger fastQ into Illumina fastQ? thanks
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Old 06-17-2011, 11:15 AM   #2
kmcarr
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Originally Posted by sunsnow86 View Post
I just got back my Hi-Seq data which use CASAVA 1.8 to process the data and the quality scores are now in Sanger format Does anyone know a script which can transfer sanger fastQ into Illumina fastQ? thanks
Since it took Illumina years to come to their senses about this and produce FASTQ in the accepted standard format can I ask why you want to go back the other way?
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Old 06-17-2011, 11:59 AM   #3
sunsnow86
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our whole downstream analysis pipeline based on the Illumina score system, so it will be easier to convert it to that format.
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Old 06-17-2011, 02:21 PM   #4
maubp
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Originally Posted by sunsnow86 View Post
I just got back my Hi-Seq data which use CASAVA 1.8 to process the data and the quality scores are now in Sanger format Does anyone know a script which can transfer sanger fastQ into Illumina fastQ? thanks
You can use several existing tools to do the conversion to/from Illumina FASTQ and Sanger FASTQ, including EMBOSS seqret, Biopython, BioPerl, BioJava, BioRuby etc.
http://dx.doi.org/10.1093/nar/gkp1137
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