Hi David, We don't have the aligned reads available; I suggest contacting the data submitter to request them. The contact information is on the track details page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm8&g=broadChromatinChIPSeq
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group David Ries wrote, On 06/24/11 06:45: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
