I'm having some trouble using RepeatMasker and was wondering if there's anyone out there that's used it before. Some of my sequencing files seem to have run just fine but the majority of files (the bigger ones especially) were clustered into their own separate folders with a lot of added results files that I can't find information about: .cat, .custom, .dat, .tmp.simple and of course a lot of .err files.
I'm getting the feeling that the masking of these files were not successful but why? Anyone seen this before? I'm using Illumina sequencing files converted to fasta format an they are round about 1G in size.