I used HTSeq-Count for counting the reads that overlap with introns and exon. I also need to count the reads that overlap with 5' or 3' splice sites not junctions. I want to count the reads that overlap 5 base pairs with intron and 5 base pairs with exon in 5' or 3' splice site. For example, if start site of my intron (5'ss) is nucleotide 20 on chromosome X, I want to count the reads that overlap from nucleotide 15 up to 24 (10 nucelotides length). I created a GTF file that have these coordinates X 16 24 5'SS, and I think what I should do is asking HTSeq-count to count 5'SS reads with minimum overlap of 10 nucleotides. However, HTSeq-count does not have option to set minimum overlapping bases. I started to use featureCount but it gives me unexpected results. When I set minimum overlap bases in featurecount to 11 or 12, that is bigger than 10 (length of 5'ss), it still reports overlapping reads. Is there a way to count the reads that overlap with few base pairs upstream and downstream of splice sites?