I am quite new to RNA-seq analysis, but what I have learned so far is that replicates are important. If you have this result with no replicates then P-values are more or less meaningless. You can also gauge what is happening by looking at the modelled read count output. If the counts are both less than 50ish you are unlikely to have a robust result for that gene/transcript. Ian ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Malik, Shivani [Shivani.Malik@ucsf.edu] Sent: 11 March 2014 21:43 To: galaxy-user@lists.bx.psu.edu Subject: [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/