ChIPpeakAnno, callEnrichedRegions results have "holes"
0
0
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
Yeast Yeast • 918 views
ADD COMMENT

Login before adding your answer.

Traffic: 606 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6