Question: ChIPpeakAnno, callEnrichedRegions results have "holes"
gravatar for Susan Wilson
7.2 years ago by
Susan Wilson50
Susan Wilson50 wrote:
Hi, I have some ChIP-seq data which returns a fairly uniform set of scores with the computeMATScore function. When I export (rtracklayer) that data as a .wig file, IGV visually reinforces that fact. However, when I run callEnrichedRegions, no matter how I try and "relax" the thresholds, using either method = score, pValue, or FDR, the resulting (bedgraph) data has single contiguous "holes" in regions of yeast chromosomes IV, X, XII, XIII, XV, and XVI (note, the chromosomes are not completely blank). The wiggle plot shows no obvious qualitative differences in those regions. Has anyone seen this behavior? Thanks. Susan
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