What software is available that allows you to use a Input normalized wiggle file as the input file to calculate the signal density within gene bodies?
Thanks.
Thanks.
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Check sitepro function in CEAS - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
If not mistaken SeqMiner accepts wig files as input... -
Seqminer does not take wig files and sitepro won't do variable spans for different coordinates. It requires a fixed span, ex: +/- 1kb from center of BED region. You can get values from CEAS but they are normalized to gene size which I do not want. I can also convert the wiggle file to BED or bedgraph and use something like bedcoverage but that just quantifies how many windows in the gene have a signal and disregards the peak size. Thanks.Comment
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