the score column of the above bed file contains $directionality = 1-($strand_diff/$strand_sum);
In other words, if $fwd_count==$rev_countthen score=1 in the bed file.
Running the demo, there is exactly 1 locus with bi-directional transcription (strand==".") and about 30 loci where the score column of the bed file is > 0.9 denoting a strand count imbalance of less than 10%. Where 5 of these loci surprisingly have a score of 1, which should mean completely balanced fwd and reverse strand counts. Such transcriptional activity seems intuitively bidirectional:
the subroutine calculateDirectionality adds a 'score' to the output file:
According to the sub, we have that
$strand_diff = abs($fwd_count-$rev_count);$directionality = 1-($strand_diff/$strand_sum);In other words, if
$fwd_count==$rev_countthenscore=1in the bed file.Running the demo, there is exactly 1 locus with bi-directional transcription (strand==".") and about 30 loci where the score column of the bed file is > 0.9 denoting a strand count imbalance of less than 10%. Where 5 of these loci surprisingly have a score of 1, which should mean completely balanced fwd and reverse strand counts. Such transcriptional activity seems intuitively bidirectional: