Entering edit mode
Susan Wilson
▴
50
@susan-wilson-2699
Last seen 10.2 years ago
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