Hi Reza, That is the main download format for those files. I looked on the PennCNV website it looks as though they recommend downloading the exact files you mention in your email (http://www.openbioinformatics.org/penncnv/penncnv_annotation.html#_Toc214862619). I recommend contacting the email address on their home page (http://www.openbioinformatics.org/penncnv/) if you are still experiencing difficulties.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/1/10 2:38 PM, Bekheirnia, Mir Reza wrote: > Hi, > > I am trying to use > knownGene.txt.gz<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz> > and > kgXref.txt.gz<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/kgXref.txt.gz> > files downloaded from UCSC to work on "Finding overlapping/neighboring > genes for CNV calls" with PennCNV, however downloaded file is not compatible > with PennCNV. I was wondering if there is any different version of these > files? > > Thanks, > Reza > > Reza Bekheirnia, MD > Clinical Fellow > Department of Molecular and Human Genetics > Baylor College of Medicine > Cell: (832)866-2273 > Email: [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
