Hello Joel, Here is a page on our genomewiki that another user added on this topic: http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
The tools are all in the Genome Browser source code, and instructions for downloading it are here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads I hope this information is helpful. Please feel free to write back to this mailing list with further questions. -- Brooke Rhead UCSC Genome Bioinformatics Group On 02/25/10 11:10, Joel McManus wrote: > Dear UCSC genome informatics group, > > I'm writing to ask how I should go about making custom liftover chain > files. I am re-sequencing the genomes of Drosophila Simulans and > Drosophila Sechellia and need to compare their coordinate positions to > that of D. melanogaster. The currently released versions of those > genome assemblies contain numerous errors and large gaps, so I'm > trying to fill those in using Illumina GAII data. > > Could you send me the programs necessary to make the liftover chain > files? I'm guessing I'll need to have pairwise alignments of each > resequenced genome with D. melanogaster as input. > > Please let me know how to go about this. > > Thank you for your time, > > -Joel. > Joel McManus > Postdoctoral Fellow > Graveley Lab > University of Connecticut Health Center > Department of Genetics and Developmental Biology > 263 Farmington Ave > ARB Rm E3053 > Farmington, CT 06030 > phone: 860 679 2092 > [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
