I’m trying to use ComputeMatrix to display ChIP-exo data for RNA polymerase II concentrated in the promoter proximal region of Drosophila genes. The problem I’m encountering is that reads on the forward strand represent the upstream border of Pol II transcribing to the right and the downstream border of Pol II transcribing to the left. The opposite is true for the reverse strand. How do I generate a matrix consisting of reads from the upstream border of all Pol II peaks. This requires tallying reads from the forward strand for Pol II transcribing to the right and the reverse strand for Pol II transcribing to the left.
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