I'm trying the tuxedo protocol as well as analysis using DESeq2, I wanted to see if I can see in the difference of DE genes. DESeq2 uses something called count matrix ,which I generated using both ht-seq and featurecounts .Now I want to know how do I transform those counts to make it usable for DESeq2 analysis
I see the count table from ht-seq and featurecount whats the difference between both the output.? for ht-seq I see a long list of ensemble ID with the counts where as for featurecount there is lot more information .
I have two 4 samples Control vs Test with replicate of each of them ,so I have the all together 4 count table.
So how can i use those counts into my DESeq2 ?
Any help and suggestion would be highly appreciated.