In this paper, we propose SVEM, a novel statistical method to detect SVs with a single nucleotide resolution that can utilize multi-mapped reads on breakpoints. SVEM estimates the amount of reads on breakpoints as parameters and mapping states as latent variables using the expectation maximization...
usage: CLAM [-h] [--version] {preprocessor,realigner,peakcaller,permutation_callpeak,peak_annotator,data_downloader} ... CLAM -- CLip-seq Analysis of Multi-mapped reads positional arguments: {preprocessor,realigner,peakcaller,permutation_callpeak,peak_annotator,data_downloader} preprocessor CLAM Prepro...
We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq ...