Dear Chu Shirly, no, reads without CpGs are not removed before calculating coverage. Only when calculating differential enrichment between conditions, windows without CpGs will not be tested, if the variable MeDIP is set to true. Please also consider our new package QSEA for the analysis of MeDIP-seq data. All the best, Lukas On 15 Oct 2016, at 22:44, chu_shirley [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User chu_shirley<https: support.bioconductor.org="" u="" 11681=""/> wrote Question: MEDIPS - do reads without CG's get filtered out prior to analysis?<https: support.bioconductor.org="" p="" 88322=""/>: Does the MEDIPS program remove all reads that don't have a CG pattern prior to analysis? I am finding two clusters within my lymphoma patients when I do unsupervised hierarchical clustering and the only significant difference that I am finding is that one group had more reads without the CG pattern. Thanks! ________________________________ Post tags: medips You may reply via email or visit MEDIPS - do reads without CG's get filtered out prior to analysis?