Many publicly available RNA-seq BAM files are mapped to a genome rather than a transcriptome (e.g. Consider the set of controlled TCGA read alignment files). Using RSEM on files such as these is problematic. How about providing a new processing mode that allows genome-oriented BAM files to be used directly?
Many publicly available RNA-seq BAM files are mapped to a genome rather than a transcriptome (e.g. Consider the set of controlled TCGA read alignment files). Using RSEM on files such as these is problematic. How about providing a new processing mode that allows genome-oriented BAM files to be used directly?