Dont use the - b parameter Sent from my iPhone; please excuse any brevity or typos!
On Nov 15, 2013, at 2:51 PM, clare Hardman <chard...@mrc-lmb.cam.ac.uk> wrote: > Hi Noa, > > Yes I did use Cufflinks so this sounds just like my problem. So how have you > dealt with the problem? > > Best wishes, > > Clare > > > > On 14 Nov 2013, at 18:17, Noa Sher wrote: > >> Hi Clare >> We just ran into a similar issue about a week ago and were debugging with >> the authors of cuffdiff >> Apparently there are issues with the -b parameter - were you using this in >> cufflinks? >> If yes - this may be the cause - we switched the order of the replicates and >> the values changed; as did PCA's of the samples, etc >> They are working on this issue for an upcoming version of cufflinks. >> I am interested in knowing whether this was indeed your problem or were you >> using a pipeline that does not include cufflinks? >> Good luck, >> Noa >> >> >> On 14/11/2013 13:13, clare Hardman wrote: >>> Hello, >>> >>> Could you please advise me on this probably naive question. When I compare >>> sample A and sample B by Ciffdiff and then separately compare Sample A to >>> Sample C by Cuffdiff too, should the FMPK value be the same for A in both >>> tests? At the moment mine does not seem to be! >>> >>> Best wishes >>> >>> Clare >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> >
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