MEDIPS - export wig with normalized counts
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lshepard ▴ 40
Last seen 6 days ago
United States


Question regarding MEDIPS.exportWIG - I see that while there is an option of exporting counts, it looks like these are the raw counts instead of the EdgeR normalized counts. Is there a way to get the normalized counts instead? Currently the closest I can get to this is by using rpkm in the format parameter, however this is suboptimal as there are differences between these two normalization units, especially given that I used diff.method="edgeR" to identify DMRs.

Also note, I am familiar with the fact that deeptools can generate bigwig directly from the BAM, and while they provide a number of normalization methods with their bamCoverage function, I would still prefer to use the normalized counts from edgeR present in MEDIPS if possible.

Any advice is welcomed!


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