Hello, Apologies for the slow reply. I've moved this thread to the galaxy-user mailing list because it centers on using Galaxy rather than developing it.

2. deleted the first files, like the first fastq files, but I'm affraid to have an error messages

Deleting your fastq files after you have mapped your reads is fine and will not cause any errors. Make sure to both delete and purge your datasets to clear them from your account: http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Delete_vs_Delete_Per...

3. to obtain more memory, just for the time of the study.

Your best bet to obtain more memory quickly is to use a cloud instance: http://wiki.galaxyproject.org/CloudMan Good luck, J.