Hello Jianpeng,

The data needs to be assigned to datatype "fastqsanger". This datatype indicates that the quality scores are scaled as Phred+33 (which they most likely are from this technology).


The tool "NGS: QC and manipulation -> FASTQGroomer" can be used with the input option "Sanger" for your data to both assign the datatype and perform format verification. Or, optionally, you could just assign the datatype: pencil icon -> Edit datasets -> Datatype tab. If you just assign, and the dataset gives errors with tools, backing up and running the groomer will often tell you exactly where in the file the problem is located (format).

Best,

Jen
Galaxy team

On 10/23/12 8:05 AM, Xu, Jianpeng wrote:
Hi All,

I am trying to use Galaxy to analyze the Ion Torrent data. I have
uploaded my data to the galaxy. However, when I try to use FASTQ Quality
Trimmer and Trim sequences to trim my fastq files, my file does not show
in the FASTQ File menu.

Do you know why ? How to fix it? Do these programs work on Ion Torrent
data ?

Thanks,

Jianpeng

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