Hi, for most of the stuff I do, I ideally need aligned reads (BED, BAM, SAM). The wig/coverage files are also okay, but they give less information. Let's say I want to perform peak calling. I am not aware of a peak finder that accepts wig files. And I can't convert wig files to aligned reads again, only to bedgraph. Additionally, those wig files are compressed, and it would be nicer to work without losing some of the information.
So is it possible to - do peak finding with wig files or - convert the wigfiles back to something like aligned reads or - get the aligned reads in the first place? But anyways, I am already very happy that I can get the data in wig format. Best, David > 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.htm > >l > >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
