Hello Gundala, To use the web version of the tool, the data must be in BED or position format. The acembly table is in genePred format. The unix version of liftOver from our cvs tree has an option for genePred format, but the web version does not. In addition, this file from the ftp location has an extra column at the beginning (what we call "bin") for database indexing that would need to be removed before using the unix version of the tool, if you attempt this at a later time.
For a web base query path, I suggest that instead of using ftp, extract the file using the Table browser and select output format as "BED". Name the file to download and save to your computer. Then, upload into the web version of the liftOver tool. I just ran an example with Table browser BED output in the web liftOver and it worked as expected. Please let us know if you additional help. Our FAQ section has many details about file formats, Table browser help, etc. http://genome.ucsc.edu/FAQ/ Jennifer Jackson UCSC Gemone Bioinformatics Group ps. Next time, please send questions directly to the mailing list for the quickest response. > Gundala Viswanath wrote: >> Hi Jeniffer and all, >> >> Following your advice I intend to convert this acembly.txt from MM9: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/acembly.txt.gz >> >> into MM8, by uploading it to this website you suggested: >> >> http://genome.ucsc.edu/cgi-bin/hgLiftOver >> >> but somehow it fails to execute. >> >> Is there a way/tool where I can convert the acembly format into BED/Position >> format acceptable for the website? >> >> >> Yours, >> Gundala Viswanath > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
