Hi Nandini, There is actually no longer a download for ldHgGene - it has been superseded by gff3ToGenePred. Can you send me a copy of the GFF file you're using (if it's not too large - or a sample of it) so we can test it?
- Greg On 11/16/11 4:44 AM, Nandini B wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
