Hi Pouya, Thank you for your interest in the UCSC Genome Browser. We are currently working on answering your question and hope to have a reply to you soon.
Thank you, Mary --------------------- Mary Goldman UCSC Bioinformatics Group On 8/24/10 2:08 PM, Pouya Kheradpour wrote: > My goal is to have both wgEncodeGencodeManualV4 and > wgEncodeGencodeAutoV4 in GenePred format. > > I tried to download the wgEncodeGencodeManualV4 table from the test > browser. For some reason when downloading it gets stuck after > downloading and the file is cutoff (chromosomes 17-22 are completely > missing, chromosome 16 is there partially; after exactly 409600b = > 400kb). This happens reproducibly across multiple > computers/networks/operating systems. I also want the > wgEncodeGencodeAutoV4, which appears to download ok. > > I have had this sort of problem before (where downloads from the table > browser would get stuck). I am not sure what causes them. Is there a url > from which the data can always be downloaded in flat files? > > I can also download the gtf version of these files from: > > http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGencode/wgEncodeGencode{Auto,Manual}V4.gtf.gz > > But when I try to convert the AutoV4 file I get several errors: > > gunzip -c wgEncodeGencodeAutoV4.gtf.gz | gtfToGenePred -allErrors > -genePredExt /dev/stdin /dev/stdout > > ... [snip] > no exons defined for 93876 > no exons defined for 93875 > no exons defined for 93874 > no exons defined for 115098 > no exons defined for 27940 > no exons defined for 29602 > no exons defined for 29603 > no exons defined for 10879 > 622 errors > > and these genes are missing from the final output (although they are > present in the wgEncodeGencodeAutoV4 I download from the test browser). > > I was wondering what the command used to convert the gtf files above to > GenePred actually was. Also, can the table browser be repaired? > > Right now I am using wgEncodeGencodeAutoV4 from the table browser and > wgEncodeGencodeManualV4 converted with gtfToGenePred, but it would be > nice to have a more consistent way to set it all up. > > Thanks, > Pouya > > _______________________________________________ > Genome maillist - Genome@lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
