rmhubley
cannot mask my fusarium assembly
How can i derive a masked version of my genome? how can i free download RepBase RepeatMasker Edition for RepeatMasker? a subscription is required in order to download RepBase, so i cannot use it. i run repeatMasker on a fusarium organism but it wasn't able to find any repeated sequences or any other element. can you suggest me what to do? should i use a specific library? if yes , where can i find it? thank you in advance, Maria gap_filled_masked.txt
RepeatMasker may be used to mask your genome, however at this time we do not have any TE families defined for Fusarium in Dfam. As you point out you may find some coverage in Repbase but we do not currently have access to it ourselves so I am not sure. You are correct that it is not available freely and you will need to obtain a subscription to use it. You may want to try developing your own library by running a de novo repeat finder such as RepeatModeler on your assembly.
