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
