Dear all I'm trying to create a liftover chain file to convert two assemblies of a fungal genome. I repeatmasked the new assembly on the repeatmasker web server with default options. faSplit to 3k chunks, blat, etc (essentially following the instructions on "Minimal_Steps_For_LiftOver" and "hg/doc/liftOver.txt").
The genome consists of a few chromosomes, all <6Mb, and repeats are mostly retrotransposons and a few tandem repeats of unknown origin. The coordinates after liftover seem to have worked well, but all the repeats were ignored. By this I mean that all annotations for repetitive elements are erased from the lifted over file. I tried to blat the assemblies without repeatmasking, but the result is an unholy mess. What steps do you recommend to create a liftOver chain file without any loss in the sequence? Thank you! Mikel _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
