Currently, if a person uses HTSeq-Count to count reads on transcript level and the tool finds a read that overlaps two overlapped transcripts (this is very common) then the tool will identify the read as ambiguous and will not include it in the counting process. As the author assumed, this is useful for identification of differentially expressed genes. However, this approach will underestimate the expression of overlapping transcripts and overestimate unique ones.
Can we modify somehow HTSeq-Count to include such reads? any other tools that overcome such situation?
Can we modify somehow HTSeq-Count to include such reads? any other tools that overcome such situation?
Comment