Fastq datasets can have many different encodings for quality scores. See here for details: http://en.wikipedia.org/wiki/FASTQ_format Many tools in Galaxy require that fastq datasets be in fastqsanger format and designated as such in its datatype. Because your data appears to be in Sanger/Illumina 1.9 format, you can simply change the datatype (click on the pencil icon to change the datatype). If you have fastq datasets in other encodings, you can use the FastQ groomer tool to convert it to Sanger format. Best, J. On Jul 18, 2013, at 9:41 PM, Ricardo Perez wrote:

Dear all,

We are doing some processes in our server that use fastq files. We have obtained the data in .sra format and then convert them into fastq format using the sra tool kit. However, when we upload this files into galaxy, some tools does not recognize the file as fastq. When we apply FasQC:Read QC, under summary statistics it says that encoding is Sanger / Illumina 1.9. Is this an error of our part while installing galaxy in our server?

Thank you for your time, --Ricardo Perez ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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