extract GO enrichment

[tinguzman]

Hi,

i'm trying to use the extract_GO_enrichment script on the trinity package. however, i'm not sure on what information to use as inputs.

--GO_annots - this is the file containing list of genes and their GO terms/ GO id

--fpkm_matrix - the fpkm matrix file, containing the gene list with fpkm values

--GO_Id -list of GO Id (txt file I guess)

--gene_factors_file -the gene factor defining the genes of interest (i'm not sure what is this, is this the differential analysis results for example, after edgeR, I have the list of genes (up regulated and down regulated) with the p-value and fdr adj values?

--factor --the gene factor defining the genes of interest?


i hope you could help me on this.


thanks,
christine