Hello Pauline, I was searching for this utility with an understanding that "ldHgGene" is a lower case "L" on this link http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
But I don’t seem to find it. I tried using the gff3ToGenePred command line utility : "./gff3ToGenePred in.gff3 out.gp " but then that as well gives me an empty out put file. Can this be used for a whole genome data ? Thank you, Regards, Nandini > Date: Mon, 14 Nov 2011 16:49:43 -0800 > From: [email protected] > To: [email protected] > CC: [email protected] > Subject: Re: [Genome] liftoverhg19tohg18 gff3 > > 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
