Hi Hiram, Yes, we created .wib and .wig files from bedGraph files which are no longer available. In our case, we are using bins around 300 bp and have seen that the bedGraph size in the database tends to be smaller than the .wig / .wib in the database and as a file. It sounds like we will have to reconstruct the bedGraph files from the BED files themselves. I was just looking for an easier way out than digging up old hard drives.
Thanks for the advice, ~Brian On Fri, Dec 3, 2010 at 6:07 PM, Hiram Clawson <[email protected]> wrote: > Good Afternoon Brian: > > Do I understand that you originally had bedGraph files which you converted > to wiggle files via wigEncode ? If that is true, you may have constructed > much larger files in the conversion than was originally in the bedGraph > files. That is not necessarily true though, it depends upon the bedGraph > data and how it was organized. The .wib files are about as condensed as > you can get for this type of data with a single byte for each data value > in the graph. However, a bedGraph data value, for example: > > chr1 0 1000 3.14 > > converts into 1,000 individual data values when converted to wiggle data. > If you had the bedGraph files, you could use them directly for the source > of the graph and in this example, 16 bytes in the bedGraph file vs. over 1,000 > bytes in the wiggle representation. However, if you had 1,000 different > data values for the positions in chr1 from 0 to 1000, the .wib representation > would remain at 1000 bytes and the bedGraph would explode to more than 16000 > bytes > for the 1,000 lines of data. A full genome sized data set in .wib > representation > would always be less than 3 Gb. bedGraph files would be immense with 3G lines > of ascii data. > > You can not return to the original data values from the wiggle compressed > single bytes. The compression changes the data which is fine for the > graph resolution, but it isn't the same data. Please note this discussion > of data types: > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > > If you have your original bedGraph files and they are smaller than the .wib > files, you could use your bedGraph files. > > --Hiram > > ----- Original Message ----- > From: "Brian J. Abraham" <[email protected]> > To: [email protected] > Sent: Friday, December 3, 2010 2:28:59 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] WIB contents and conversion into bedGraph > > Hello, > > I am running a local mirror of the UCSC browser and am coming very > close to reaching storage capacity. We went through a phase where we > uploaded local tracks in the .wig / .wib format by creating these > files via wigEncode. We have come to conclusion that the > 1GB per > track cost is too high for the resolution and our use. Is there a way > to reconstitute bedGraphs directly from the .wig / .wib files or from > within MySQL? Are we taking storage hits for both the .wib file and > what is contained in the database? > > Many thanks, > ~Brian J. Abraham > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
