Dear Biostars,
I am trying to calculate conservation scores for overlapping sense and anti-sense pairs of transcripts. Previously I used phastcons scores from ENCODE(mm9) to calculate conservation but irrespective of strand. Now I see that some times lncRNAs overlap protein-coding genes in an anti-sense manner. These lncRNAs are showing high levels of conservation because of its overlap. Therefore I am wondering is there any way to calculate conservation scores based on a strand ?
Thanx in advance