Hello Irene, This wiki has the formatting details, including a screencast for genome prep, and many tips for correcting format problems that use Galaxy's tools whenever possible: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes#Screencasts_.26_Tutorials watch "Custom Genome Prep" http://wiki.g2.bx.psu.edu/Learn/CustomGenomes#Troubleshooting That said, it many simply be that the "datatype" is not actually set to be "fasta" for the dataset? Do this by clicking on the pencil icon to reach the "Edit Attributes" form, set this manually, and save. Hopefully this helps, Jen Galaxy team On 8/10/12 3:39 AM, i b wrote:

Dear all, I managed to upload to Galaxy a genome of interest in .fasta format from NCIB website.

However, Galaxy does not recognize it as input to run Tophat...

Wht format has to be to be used as referece genome for tophat?and how can i convert it?

Any suggestion?

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