Hello Diogo, A better method for getting your data would be to directly download the tables you are interested in and query them locally, or to use our table browser
To download the tables and query them locally you can go to our downloads area and find the tables of interest: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ Alternatively, you can go to the table browser (http://www.genome.ucsc.edu/cgi-bin/hgTables) and select: group: Pilot ENCODE Chromatin Immunoprecipitation track: Sanger ChIP table: (your tables of interest) You can then select region: genome, and output format: all fields from selected table to download the whole tables. You can also restrict the output to selected regions of the genome by changing your selection in the "region" field, and you can change the output format depending on whether you want data points or table format etc. 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 Diogo FT Veiga wrote: > Hi Genome Browser team and all, > I'm trying to get the Encode histone modification data (Sanger Chips > tracks), but something is going wrong. The score element is coming empty in > the XML files, like this: > > <FEATURE id="encodeSangerChipH3K36me3.chr7.117280115" > label="encodeSangerChipH3K36me3"> > <TYPE id="encodeSangerChipH3K36me3" category="other" > reference="no">encodeSangerChipH3K36me3</TYPE> > <METHOD></METHOD> > <START>117280116</START> > <END>117280352</END> > <SCORE>-</SCORE> > <ORIENTATION>0</ORIENTATION> > <PHASE>-</PHASE> > <GROUP id="encodeSangerChipH3K36me3.chr7.117280115"> > <LINK href=" > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:117280115-117280352&db=hg18";>Link > to UCSC Browser</LINK> > </GROUP> > </FEATURE> > > > DAS URL: > http://hgwdev-gencode.cse.ucsc.edu/cgi-bin/das/hg18/features?segment=7:115404471,117281897;type=encodeSangerChipH3K36me3 > > This is happening for all "encodeSangerChipsXXX" queries. Exception to > "encodeSangerChipH3K4me(1,2,3)" for which I could get score data. > > Anyway to fix this? Is there an alternative DAS server providing Sanger > data? > > I appreciate any suggestion > > Thank you, > Diogo > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
