I am having a trouble understanding HT-seq Counts. I have a first strand library (dUTP). This data was previously analyzed incorrectly using the option stranded = Yes by someone else. I have reanalyzed it with Stranded = Reverse which is the correct option. Here is a subset of the count table from one sample:
Gene Stranded = Yes Stranded = Reverse ENSDARG00000000001 7 114 ENSDARG00000000002 12 37 ENSDARG00000000018 28 1047 ENSDARG00000000019 24 1236 ENSDARG00000000068 8 308 ENSDARG00000000069 17 1014 ENSDARG00000000086 25 88 ENSDARG00000000103 98 4159 ENSDARG00000000142 2 98 ENSDARG00000000151 1 34
Can someone please help me understand how HT-seq count is doing the counting. Why does using stranded =Reverse with the data set produce more read counts than Stranded = Yes. I need to be able to understand the underlying reason why the counts are so different.