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
