Hello Rayann, The procedure to create a liftOver input is multi-stepped.
Specifically, the Chain and Net track data are first created and then converted to a file "over.chain" that is used as one input to the liftOver program. The second input to the program would be the coordinates to convert (BED format). LiftOver goes in one direction only, so you probably would need to do both. At that stage, you may also want to do some reciprocal-best type of filtering, depending on your analysis goals. The first step is to download and install the UCSC source code. README files in the source explain how to set up your environment, compile utilities, etc. http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 Next, examine the procedure in jksrc/kent/src/hg/doc/liftOver.txt Online version: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt From there, the advice/links in this prior question/answer should help with some of the details for creating "best hit" types of files. https://lists.soe.ucsc.edu/pipermail/genome/2009-April/018821.html Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/28/10 2:17 AM, rayann siri wrote: > > Hello, > I make a study on a comparative analysis of two genomes of Arabidopsis, it > involves about an analysis of the dynamics of their transposable elements, to > be more precise. > Within the framework of this study, I aligned (with Mummer) and annotated > both genomes. > I have, thus, the coordinates of these transposable elements on one of the > genomes, that I shall want to convert on the other one. > For that, I'd like to use LiftOver, for the first time. > Is it possible to make that, with LiftOver, if yes, I'd like to know how I > can do, and what are the steps. My transposable elements coordinates are in > GFF format and BED format, with only 3 columns for the BED format (Name of > scaffold or chromosome, the Start and End). > Thank you for your assistant > _________________________________________________________________ > Hotmail et MSN dans la poche? HOTMAIL et MSN sont dispo gratuitement sur > votre téléphone! > http://www.messengersurvotremobile.com/?d=Hotmail > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
