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
