Good Morning Mikel: What do you mean masking out the repeats ? What procedure do you use for that ?
blat by default does not use the lower case repeat masking information in the sequences. You would have to specify that to make it use that masking information. The blat command arguments we use to construct the lift over alignments are: -tileSize=11 -ooc=targetOrganism.11.ooc -minScore=100 -minIdentity=98 -fastMap --Hiram Zaratiegui, Miguel wrote: > 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
