 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.
The output of both HT-seq and featurecounts can *almost* be fed directly in DESeq2.

 - **for FeatureCounts :**

Output looks like :

    Geneid	Chr	Start	End	Strand	Length	cond1	cond2
    SPBC460.05	I	16470	18062	+	1593	1	12	24
    SPBC460.02c	II;II	8856;9651	9365;9803	-;-	663	329
    SPAC212.11	I	1	5662		-	5662	0	0	0

First you need to remove 5 firsts columns and name the rows as gene names


    	cond1	cond2
    SPBC460.05	12	24
    SPBC460.02c	663	329
    SPAC212.11	0	0

then just use the `DESeqDataSetFromMatrix` function of DESeq2 to convert it.

 - **for HTseqCounts :** see comments below