NormGAM: an R package to remove systematic biases in genome architecture mapping data.

ABSTRACT: BACKGROUND:The genome architecture mapping (GAM) technique can capture genome-wide chromatin interactions. However, besides the known systematic biases in the raw GAM data, we have found a new type of systematic bias. It is necessary to develop and evaluate effective normalization methods to remove all systematic biases in the raw GAM data. RESULTS:We have detected a new type of systematic bias, the fragment length bias, in the genome architecture mapping (GAM) data, which is significantly different from the bias of window detection frequency previously mentioned in the paper introducing the GAM method but is similar to the bias of distances between restriction sites existing in raw Hi-C data. We have found that the normalization method (a normalized variant of the linkage disequilibrium)

SUBMITTER: Liu T 

PROVIDER: S-EPMC6936146 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature