These are options we'd like to add to Cufflinks, and I've created a Trello card for this enhancement: https://trello.com/c/U7nceKdj I want to add that community contributions via patch or pull request are highly encouraged and are likely to be quicker than waiting for the core team to get to this issue. Best, J. On May 29, 2013, at 8:47 AM, Nikolay N. wrote:

Hi,

Most people using the RNA-Seq toolkit use a combination of Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use different normalisation schemes (http://seqanswers.com/forums/archive/index.php/t-26041.html). Users overcome this problem by running cufflinks with the following flags:

--compatible-hits-norm --max-frag-multihits 1

However, in galaxy it is not possible to run cufflinks with these flags. Can you, perhaps, add support for them?

many thanks, Nikolay ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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