Hi , I am trying to use the stitch MAF block tool with my bed file for rat genome (rn6) but it asked me for the MAF source and type. I went into the edit dataset and set my database to rn6 but it doesn't seem to help. How can I make it work ?
Both the input interval dataset and the input MAF dataset (from your history, it is not natively indexed) should have the database and datatype set (one is interval, the other maf).
MAF datasets for rn6 are available from UCSC. Load the data from the downloads area (under "Conservation" per genome) via URL - these are too large to load from the UCSC Table Browser. Just be aware that these are large files - so you may need to make room on your account to load/use them (free of space by permanently deleting unneeded datasets - you can always download these first to keep a copy).
Thanks, Jen, Galaxy team