Hi David, Can you specify what format you need? It may be possible to change the current data format into the format that you need with a few scripting lines. The original paper's authors may also have the data in a format that would be useful to you; please feel free to contact them as well.
Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/21/11 2:39 AM, David Ries wrote: > Hi Katrina, > > thanks, that already helped a lot. > I could extract the data as wiggle format with the -doAscii option, > and as bed format with -doBed. > The wig format is compressed, and the bed format seems to be giving the bound > regions. > Is it possible to get the data in an uncompressed version? Something which > equals the aligned reads? > Many programs I work with (like if I want to do peakcalling my own), cannot > use variableStep wig data. > > Best regards, > > David > > > Hi David, > > > > You can download this data as BED files using our Table Browser. >>> However, if you are downloading more than just a small portion of >>> this >>> data, this would be an inefficient method. Also, for the Signal data, >>> using the table browser results in the data being compressed with a >>> minor loss in resolution. > > > Please see this previously answered mailing list question about >>> extracting data from these types of tracks and help with hgWiggle: > > > https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024495.html > > > > This is the location of the data you will need for the directions: >>> ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/ (the files >>> called broadStemChip*) >>> ftp://hgdownload.cse.ucsc.edu/gbdb/mm8/broadStemChip/ > > > I hope this is helpful. Please contact the mail list >>> ([email protected]) again if you have any further questions. > > > Katrina Learned >>> UCSC Genome Bioinformatics Group > > > > > David Ries wrote, On 6/17/2011 7:13 AM: > > Hello, > > > > I'm interested in working with the Broad H3 mm8 Data, as it can be >>>> viewed in >>>> the UCSC browser. >>>> Is it possible to get this data as wig or BED format? >>>> I tried to extract it with hgwiggle out of the wib files, but it >>>> didn't work >>>> for me. > > > I realized, that the H3 tracks for human can easiely be downloaded, >>>> but for >>>> mouse it's not the case. > > > Any help would be much appreciated. > > > > Best regards, > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
