Hello,

To clarify, you wish to go from CASAVA 1.8+ ( Phred+33) quality scores to the older version 1.3-1.7 ( Phred+64) quality scores?

This is possible with the "FASTQ Groomer" tool with the "Advanced Options".

Please be aware that most, if not all, of Galaxy's tools are designed to work with Phred+33 scaled quality scores (e.g. "Sanger"). Illumina output could be originally Phred+33 or Phred+64 depending on when it was generated and which software was used to post-process the data (CASAVA 1.3-1.7, 1.8+). Your source should be able to tell you what the data content is. It can be tricky to guess, although the sequence headers can sometimes be a clue. The wikipedia link on the Groomer tool has a very good explanation of this. The Groomer tool's output "Info" comments will also provide some feedback about valid quality score ranges vs the tool options used, after processing.

For most users, when using the "FASTQ Groomer" tool, the goal is to get the data into "Sanger Phred+33" format. Even if the data is already in "Sanger" format, the Groomer tool can be used to catch format problems, although directly changing the datatype to ".fastqsanger" is also OK (for the tools that require this datatype in order for the dataset to be recognized; not all do).
* If the input is CASAVA 1.3-1.7, this is Phred+64, and the "Input FASTQ quality scores type: Illumina 1.3-1.7" should be used.
* If the input is CASAVA 1.8+, this is Phred+33, and the " Input FASTQ quality scores type: Sanger" should be used.

Hopefully this helps,

Jen
Galaxy team

On 5/11/12 7:30 PM, shamsher jagat wrote:

I want to convert Sanger FASTq to Illumina FASTq with a understanding that Sanger is the current option with CASAVA. Is it possible to do such conversion in Galaxy?

Thanks

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