dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run cufffidff. in cuffdiff output for studying which genes are differntially expressing what all parameters should be taken care of. i came across one thing from other posts that p value < .05. what other facotrs i should look for before filtering my genes of interest. significant column?? if it says no and p value is less than .05 then can i take that. also how to interpret from promoter diffenrential expn file and tss differential expn file. thanks in advance
Ignore the p-value, you want the q-value instead (this is the p-value adjusted for multiple testing). The "significant" column will then correspond to the q-value. In addition, you may want to filter according to the fold-change (log2(FPKMy/FPKMx)), since values closer to 0 are less likely to be biologically interesting.
Unless you have a burning question, I would suggest only looking at the gene-level differences. All the other stuff is best ignored (both because it's less reliable and also because it's hard to determine what it would biologically mean).