I have two questions about the output from CuffNorm:
1) Why is there an unlabeled row (with values) at the beginning of the genes.fpkm_table file? I thought perhaps the gene column had gotten shifted down one, but the last line has gene99999 and values for all of my samples, whereas the first value line of this file has nothing in the first column and values for my samples. Does anyone know what this row is or if there is a way to fix the problem?
2) The first row of this file, which contains the headers (sample names), has replaced my sample names with M1_0, M1_1, M1_2, etc. and has reordered them. So, I have two sets of samples, five of which are M1 cells and five of which are M2 cells. Are the M1_0, M1_1....in the same order as the list that I told the program to use? Here's what I mean:
This is my command line: cuffnorm -o CuffNorm_Out -p 20 -L M1,M2 MouseGFF.fa ./M1_1_3.cq/abundances.cxb,./M1_2_13.cq/abundances.cxb,./M1_2_14.cq/abundances.cxb,./M1_2_15.cq/abundances.cxb,./M1_2_17.cq/abundances.cxb M2_1_2.cq/abundances.cxb,./M2_2_8.cq/abundances.cxb,./M2_2_23.cq/abundances.cxb,./M2_2_24.cq/abundances.cxb,./M2_2_26.cq/abundances.cxb
Does M1_0 = M1_1_3 and M1_1=M1_2_13? Also, the output file has reordered them so that the first row says: tracking_id M1_0 M1_1 M1_4 M1_3 M1_2 ...........
I appreciate any and all advice you can offer!