Hi, Yes, if your old file is in gff format, the new file is also in gff format.
Note that the liftOver program usage statement says: > -gff File is in gff/gtf format. Note that the gff lines are converted > separately. It would be good to have a separate check after this > that the lines that make up a gene model still make a plausible gene > after liftOver This means that each part of a gene in gff format will be run through liftOver separately. The potential problem is that different parts of the same gene may be lifted to totally different locations in the new assembly. If you are okay with that caveat, then gff format is okay for you. If you would rather ensure that an entire gene is lifted as a unit, you need to convert it to a different format, such as genePred or BED. See descriptions of various file formats here: http://genome.ucsc.edu/FAQ/FAQformat.html The warning message you saw gives one way to convert your gff file into a genePred file: > WARNING: -gff is not recommended. > Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>' It is referring the command-line utility available in the source tree (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads) called ldHgGene. The utility will convert your gff file to a genePred file. Alternatively, if you don't have the source tree already, an easier way to convert the file would be to upload it as a custom track, here: http://genome.ucsc.edu/cgi-bin/hgCustom Then go to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), select the custom track you just made, choose "region: genome" and "output format: BED". Enter a filename in the "output file" field to download the file to your computer. If you use the genePred or BED version of your file, you will not get the warning about gff files. -- Brooke Rhead UCSC Genome Bioinformatics Group On 03/12/11 00:34, [email protected] wrote: > Hi, > As oldfile is gff file > I used liftOver as below > "./liftOver alltrans.gff -gff mm5ToMm8.over.chain newfile.bed unmapped" > but the proagramm gave some warning of "gff" > How do I next? > Is gff format file ok? > According to the userguid, gff is ok > > Another question, I want to know, if my oldfile is gff, is new file gff, > too? > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
