[galaxy-user] Cuffdiff output
Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in no? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data? Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable? Thanks Shivani ___ 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/
[galaxy-user] Installing tool in galaxy on cloud
Hi All, I want to use Tophat2 on amazon cloud. I could not find it in the regular tools unlike the public server. Am I using the right version? I tried installing it through admin on cloud .Though I was able to make myself admin through cloudman instance , I could not see any admin panel on Galaxy main page. What am I doing wrong?Any help is appreciated. Thanks. Shivani ___ 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/
[galaxy-user] Install tools from Toolshed
HI, I am trying to install Deseq from the toolshed. I get the message:Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable cookies in your browser. I have enabled the cookies and tried both on Firefox and Chrome but could not get it to work. Can you help me on this? Thanks Shivani ___ 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/
