I'm trying to find coverage and %calls at every bp in my resulting sequencing data. I chose MIRA because of this wonderful TCS file which is suppose to provide all this information, but after running the assemblies my file states "TCS output currently not available, please contact author". I did a mapping assembly. I'm not sure if TCS can be done with mapping assemblies. Has anyone else had this problem? Am I missing an option?
Has anyone tried using caf2tcs to force convert the caf file to tcs? or maf2sam?