The limit for Tophat will most likely not be the number of reads, but
the total processing time when using the public Galaxy instance.
Currently, a job has 72 hours to complete, assuming that there is not
memory problem before that time limit is reached.
But, there are some size limitations. Initial upload file size must be
50G or less. Output files must be 200G or less, and there must be room
on your history for the output, or further work will not be possible
until the account is brought back under quota (250G).
These wikis contain the same information and more:
http://wiki.galaxyproject.org/Main -> links to ->
For large or batch processing, the cloud option is the best
recommendation, since this allows you to customize resource as needed.
Galaxy Support and Training