Hello Miro, It sounds like perhaps the datatype is not being assigned correctly, which may mean that they quality scores are not scaled properly. To double check both, see the instructions in our wiki here: http://wiki.galaxyproject.org/Support#Dataset_special_cases If you still need help after this, please write back to share a history, Best, Jen Galaxy team On 11/29/13 5:49 AM, miroslav.sotak wrote:

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to "history" and according to RNA-seq Analysis Exercise provided by Jeremy. We checked the type of Ascii ofset for the quality estimation. I tried even "quality data converter" set to 33 (we do have data of this ASCII offset from 2 different sources) but "tophat for Illumina" simply can not read the data before and even after quality format converter. We do not have any idea what is going on. I am logged in Galaxy with current email, can you check my data and is there any converter for quality offset?

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