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 (genome@soe.ucsc.edu) 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: >> genome@soe.ucsc.edu. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ---------- Forwarded message ---------- >> From: Dr. rer. nat. Volkhard Seitz<volkhard.se...@charite.de> >> Date: Thu, Nov 3, 2011 at 12:46 AM >> Subject: [Genome] Problems to up-load large bed files (Internal Server >> Error E 500)] >> To: genome@soe.ucsc.edu >> >> >> 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 - Genome@soe.ucsc.edu >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist - Genome@soe.ucsc.edu >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
