I have use the ballgown for differential gene expression. I have the six sample in my data set. The final list of differential gene expression obtain from the ballgown contain no sample name information from which I can calculate the number of DE gene in corresponding samples. The list is as
feature id fc pval qval 1 gene MSTRG.54886 0.304864331 2.14E-11 7.36E-07 2 gene MSTRG.20291 0.317939083 3.50E-07 0.005305344 3 gene MSTRG.28511 0.188768117 5.69E-07 0.005305344 4 gene MSTRG.54860 0.207911219 7.11E-07 0.005305344 5 gene MSTRG.69745 0.24928575 7.71E-07 0.005305344
how I can get the information number of differential expressed genes in one sample and so in second , third and so on . Next question is that I want to plot the van diagram of this data set of DE genes. how I can do it.