Does anyone know how to remove repetitive elements from a genome masked with RepeatMasker? What I'm trying to do is get an estimate of the fraction of the reference genome covered with Illumina reads from two mapping runs with BWA: the first run not taking into account repetitive elements and the second with repetitive elements removed so that I have an estimate of the fraction covered of the 'mappable' regions of the genome.
The masked regions are in lower case while the rest is in upper case. I thought I could just use 'find and replace' to remove the lower case bases but I can't open genome size files in my text editor.
Hope this makes sense and thanks in advance.