[galaxy-user] a question about cuffdiff values

Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of early embryonic gene expression in zebrafish embryos. After attending the Galaxy meeting I returned home and worked up two mRNAseq files to determine RNA expression differences using cuffdiff between

Re: [galaxy-user] a question about cuffdiff values

Hi El, 1) what do these numbers represent? FPKM values for sample 1 and 2. Cufflinks documentation is the place to get definitions for all columns: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 2) If in the value column where I expect a higher number has a value of 10 or less

[galaxy-user] how to use user-defined reference?

Hi everyone, I am wondering if I can use user-defined reference instead of selecting the reference genome listed in Galaxy while doing mapping. If we can, how can I choose the uploaded reference instead of selecting the reference genome? Any ideas are greatly appreciated! Cheers, Yan