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
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
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