When I am running cuffnorm (from cufflinks) on some RNA-Seq BAM files with the GENCODE v19 annotation, I do get out several outputs, most notably
When I look into these files I do obtain something like
tracking_id q1_0 q2_0 ENSG00000000003.10 4.46257 2.81516 ENSG00000000005.5 0 0 ENSG00000000419.8 58.9657 73.9058 ENSG00000000457.9 9.86299 5.55451 ENSG00000000460.12 20.4105 9.2218 ENSG00000000938.8 0.01044 0.0226546 ....
for the genes files and something like
tracking_id q1_0 q2_0 ENSG00000000003.10 0.139293 0.00827424 ENSG00000000005.5 0 0 ENSG00000000419.8 0.43631 0.520737 ENSG00000000457.9 0.440151 0.236529 ENSG00000000460.12 0.0721438 0.0884936 ENSG00000000938.8 0.000730916 0.00195449 ... ENST00000000233.5 179.357 91.6825 ENST00000000412.3 58.6248 75.4492 ENST00000000442.6 23.4939 13.6916 ENST00000001008.4 238.631 382.162 ENST00000001146.2 0.0702716 0.0796778 ...
for the isoforms.
So we do see that the genes are incorporated into the isoforms FPKM file. Here, however, the values are very close 0 and in particular different from the respective values of the genes FPKM file.
Why at all these gene FPKM values are appearing in the isoform FPKM file as well?
Why are they basically 0 and hence different from those values of the gene FPKM file?
Did I do something wrong and, if so, how do I fix it?
Many thanks for your help in advance!