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
