Hi Volkhard, A custom track containing a bigBed file is not submitted to us; the bigBed file remains on your web accessible server (http, https, ftp), not on the UCSC server. Once you have uploaded the bigBed file to an http, https, or ftp location, please follow the instructions mentioned by my colleague below.
Contact us again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 11/8/2011 1:44 AM, Dr. rer. nat. Volkhard Seitz wrote: > Dear Katrina, > thanks for your Email. > > Could you write me more details for a http, https or ftp location I can > use to get the large files up-loaded (All smaller files up to 200.000 Kb > work fine with a direkt up-load). > > I found: ftp://hgdownload.cse.ucsc.edu/goldenPath/ > > However, I need login information to up-load the files there > > Thank you and kind regards from Volkhard > > > >> Hi Volkhard, >> >> I just wanted to follow-up with some additional guidance. >> >> To use a bigBed file for a custom track, it cannot be compressed; so, if >> your file is compressed (.bz2) you'll need to uncompress it. >> >> Also, when creating a custom track with a bigBed file, you don't submit >> the actual file to us. Instead, you first move your bigBed file >> (myBigBed.bb) to a http, https, or ftp location. Then you create a singe >> track line that provides the location of your bigBed file. The most >> basic version of the "track" line will look something like this: >> >> track type=bigBed name="My Big Bed" description="A Graph of Data from My >> Lab" bigDataUrl=http://myorg.edu/mylab/myBigBed.bb >> >> You then paste this track line into the text box of the custom track >> page (http://genome.ucsc.edu/cgi-bin/hgCustom) and submit. >> >> For further information, on bigBed custom tracks see: >> http://genome.ucsc.edu/goldenPath/help/bigBed.html >> >> For more information on custom tracks in general, see: >> http://genome.ucsc.edu/goldenPath/help/customTrack.html >> >> Please contact the mail list ([email protected]) again if you have any >> further questions. >> >> Katrina Learned >> UCSC Genome Bioinformatics Group >> >> >> >> On 11/3/11 12:31 PM, Vanessa Kirkup Swing wrote: >>> Hi Volkhard, >>> >>> It is likely that this is issue "Unrecognized format line 1" is the >>> result >>> of line breaks in the track line. Please take a look at step 7 on the >>> page >>> below: >>> >>> http://genome.ucsc.edu/goldenPath/help/bigBed.html >>> >>> All of the information has to be on a single line. Please make sure that >>> you have it in the proper format. >>> >>> If you have further questions, please contact the mailing list: >>> [email protected]. >>> >>> Vanessa Kirkup Swing >>> UCSC Genome Bioinformatics Group >>> >>> ---------- Forwarded message ---------- >>> From: Dr. rer. nat. Volkhard Seitz<[email protected]> >>> Date: Thu, Nov 3, 2011 at 12:46 AM >>> Subject: [Genome] Problems to up-load large bed files (Internal Server >>> Error E 500)] >>> To: [email protected] >>> >>> >>> Dear UCSC team >>> >>> Two days agou I tried today for hours to up-load ChIP-Seq bed-files. >>> >>> I can upload files up to 200.000 KB >>> >>> Since I could not up-load a file with 812.136 KB I used now a >>> compression method you recomended an created a .gz file with 189.216 KB >>> (The filename was: C_Hodg_Ip_Kmh2_.gz) >>> The upload of this compressed .gz file caused the internal server error >>> 500. >>> >>> After writing to your team From I got the recommendation to convert my >>> file into the Bigbed format. >>> http://genome.ucsc.edu/goldenPath/help/bigBed.html >>> >>> >>> The next day I converted a bed file into a bigbed file employing galaxy. >>> The original file had a size of 856.831 KB and the converted bigbedfile >>> 245.056 kb respectively. >>> >>> The conversion report from Galaxy sounded fine: >>> >>>> 13: BED-to-bigBed on data 12 239.3 Mb >>>> format: bigbed, database: hg19 >>>> Info: pass1 - making usageList (25 chroms): 55588 millis >>>> pass2 - checking and writing primary data (14673975 records, 6 fields): >>>> 141460 millis >>>> index write: 28 millis >>>> pass3 - writeReducedOnceReturnReducedTwice: 66343 millis >>>> further reductions: 9811 millis >>>> >>> However I still have the up-load problems for the UCSC Browser >>> >>> I got the following error measages employing different file formats or >>> file names (compressed and non-compressed): >>> >>> >>> 1) File 'KMH2MYCIP.bigbed.bz2' - Unrecognized format line 1 of >>> somefile.bz2: ëò?? (note: chrom names are case sensitive) >>> >>> 2) File 'KMH2MYCIP.bz2' - Unrecognized format line 1 of somefile.bz2: >>> ëò?? >>> (note: chrom names are case sensitive) >>> 3) Can't read file: KMH2MYCIP.bigbed >>> >>> Could you five me other suggestions how I can up-load files. >>> Would be really great. >>> Thank you and best wishes from Volkhard >>> >>> >>> >>> >>> _______________________________________________ >>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
