Hi Jianguang,

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 a 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 ->
http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Data_size_and_disk_Quotas

For large or batch processing, the cloud option is the best recommendation, since this allows you to customize resource as needed.
http://usegalaxy.org/cloud

Thanks!
Jen
Galaxy team

On 3/27/13 10:38 AM, Du, Jianguang wrote:

Hi All,

Is there a size limit of dataset for running Tophat at Galaxy? If there is, how many reads is the limit?

Thanks.

Jianguang



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The Galaxy User list should be used for the discussion of
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