Hello Nandini, I am not sure if this is the issue but the first letter in the ldHgGene utility is a lowercase "L". Is it possible you were searching for one starting with an uppercase "i"?
Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/7/11 5:11 AM, Nandini B wrote: > Hello, > > I am trying to use liftOver to convert my data fron hg19 to hg18 in gff3 > format and get the output in gff3 format itself. I get an error message.> > .... >> WARNING: -gff is not recommended. >> Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred<file.gp>' > In some archived posts, I saw that I need to download the 'ldHgGene' > command line utility and the link given was > > http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads > > But somehow ldHgGene does not exists. > > I tried using the gff3ToGenePred command line utility : "./gff3ToGenePred > in.gff3 out.gp " > but then that as well does not give me an output. It just says "GFF3: 49 > parser errors" > > Could you please suggest how do I go about this ? > > > > Thank you, > Warm Regards, > > Nandini > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
