Hi Diego, Most of our bigBed/bigWig/bam files used by our database entries are available via URLs somewhere in the hierarchy: http://hgdownload.cse.ucsc.edu/gbdb/
The files that you see in the database schema, for example: /gbdb/some/path/name.bigFile can be found on our downloads site: http://hgdownload.cse.ucsc.edu<http://hgdownload.cse.ucsc.edu/gbdb/some/path/name.bigFile>by adding the file path found in the database schema to the URL like this: http://hgdownload.cse.ucsc.edu/gbdb/some/path/name.bigFile If you download the source code, there are utilities that can use the URL path names. The utilities are listed here: http://genomewiki.ucsc.edu/index.php/Kent_source_utilities and all the ones that start with "big" you are able to utilize the URL path names. bigBedSummary:Extract summary information from a bigBed file. bigBedToBed:Convert from bigBed to ascii bed format. bigWigInfo:Print out information about bigWig file. bigWigSummary:Extract summary information from a bigWig file. bigWigToBedGraph:Convert from bigWig to bedGraph format. If using these utilities interest you, you can download the source code from this page: http://genome.ucsc.edu/FAQ/FAQlicense.html#license3 Our files are all for public use with the exception that there are some restrictions regarding the publication of ENCODE data. Information regarding the publication restrictions for ENCODE data can be found here: http://genome.ucsc.edu/ENCODE/terms.html I hope this helps to clarify things for you. If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Diego F. Pereira <[email protected]> Date: Tue, Nov 29, 2011 at 2:06 PM Subject: RE: [Genome] Hg19 tables To: Vanessa Kirkup Swing <[email protected]> Cc: [email protected] Few more questions about this topic... The aforementioned files (bigBed, BigWig and bam) are intended to be used just internally by the UCSC people or external users like me can do something with them? If the last is true, where can I find information about the usability? Thanks, Diego -----Original Message----- From: Vanessa Kirkup Swing [mailto:[email protected]] Sent: Thursday, September 15, 2011 2:02 PM To: Diego F. Pereira Cc: [email protected] Subject: Re: [Genome] Hg19 tables Hi Diego, bigBed is also another file type that we store as a file in a table. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group On Thu, Sep 15, 2011 at 11:44 AM, Diego F. Pereira <[email protected]> wrote: > Thank you very much Vanessa. > Best, > Diego > > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: Thursday, September 15, 2011 1:28 PM > To: Diego F. Pereira > Cc: [email protected] > Subject: Re: [Genome] Hg19 tables > > Hi Diego, > > The tables list a path to a file name. We have 2 different types of > files types that we store as files in tables which are bigWig and bam. > To find more information on those file types please take a look at > this > page: > > http://genome.ucsc.edu/FAQ/FAQformat.html > > I hope this information is useful. If you have further questions, > please contact the mailing list: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Diego F. Pereira <[email protected]> > Date: Thu, Sep 15, 2011 at 9:23 AM > Subject: [Genome] Hg19 tables > To: [email protected] > > > Good morning, > > By reviewing the Hg19 database, I found several wgEncode tables that > have just 2 fields (i.e. fileName and Field0). > > I would like to ask you what type of information they contain or where > I can find some info about them. > > > > Best Regards, > > Diego > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
