I have finished my test run of RNA-Seq analysis with Tuxedo suite tools.
According to Panther: "The first column must be the gene or protein identifiers. See below for the supported IDs. A second column of numerical values is required if a user wants to run the statistical enrichment test."
(1) Are there suggested commands for making Cuffdiff's output into the ID list for Panther?
(2) Also, I assume the first column should be
gene column but I am not sure about the what should be the numerical values in the second column? Should I use htseq to get the number of reads pre gene?