Hi Galt, I am not sure how to add the track information to the .bw file. Shall I use the following command? cat track_info_file old.bw > new.bw Regards, Peng On Tue, Aug 4, 2009 at 8:23 PM, Galt Barber<galt at="" sundance.cse.ucsc.edu=""> wrote: > > please see step 7 of > ?http://genome.ucsc.edu/goldenPath/help/bigWig.html > > You need to do this: > > at the add custom track form, type in the track name etc., > and supply the parameter dataUrl pointing to your > binary bigwig test.bw, i.e. > > track type=bigwig name="someName" {other params go here} > ?dataUrl=http://chalk.brc.bcm.edu/wl1/pengy/test.bw > > This track line is a single line, and it can be long. > > (sometimes special characters in the dataUrl value may requre > url-encoding) > > -Galt > > > On Tue, 4 Aug 2009, Peng Yu wrote: > >> Hi Jennifer, > > Please see my .wig file and the script to generate the .bw file below. > > Then, I went to http://genome.ucsc.edu/cgi-bin/hgGateway and click > 'add custom track". In "genome" selection box, I chose "mouse". And I > chose "July 2007" assembly. > > I input the following address in the box under "Paste URLs or data:" > > http://chalk.brc.bcm.edu/wl1/pengy/test.bw > > Then, I click "submit". It gives me the following error message. > > ? ?Error Unrecognized format line 1 of > http://chalk.brc.bcm.edu/wl1/pengy/test.bw: &? ? ?(note: chrom names > are case sensitive) > > Would you please follow the procedure and see what the problem is? > > Regards, > Peng > > $ cat test.wig > variableStep chrom=chr10 span=10 > 3001501 1 > 3001511 1 > 3001521 1 > 3001531 1 > 3001541 1 > 3001551 1 > 3001561 1 > 3001571 1 > > $ cat run.sh > #!/usr/bin/env bash > fetchChromSizes mm9 > mm9.chrom.sizes > wigToBigWig test.wig mm9.chrom.sizes test.bw > > > On Tue, Aug 4, 2009 at 11:59 AM, Jennifer Jackson<jen at="" soe.ucsc.edu=""> wrote: >> >> Hello, It appears that your track definition lines is not formatted >> correctly Please see the instructions at this help page, specifically item >> #7: http://genome.ucsc.edu/goldenPath/help/bigWig.html Try the adjustment >> and please let us know if you continue to have problems Thank you, Jen >> >> ps. Attachments are not posted to the mailing list, so pasting some >> example data into an email was an excellent idea. In the future, you can >> also mention that you have example to share in file format. We can make >> arrangements to obtain the file(s) off the list. >> >> ------------------------------------------------ >> Jennifer Jackson >> UCSC Genome Bioinformatics Group >> >> ----- "Peng Yu" <pengyu.ut at="" gmail.com=""> wrote: >> >>> From: "Peng Yu" <pengyu.ut at="" gmail.com=""> >>> To: genome at soe.ucsc.edu >>> Sent: Tuesday, August 4, 2009 8:32:33 AM GMT -08:00 US/Canada Pacific >>> Subject: Re: [Genome] "Error Unrecognized format line 1..." when using >>> "Add Custom Tracks" >>> >>> On Mon, Aug 3, 2009 at 8:13 PM, Peng Yu<pengyu.ut at="" gmail.com=""> wrote: >>> > Hi, >>> > >>> > I want to add the attached file in the following webpage. >>> > >>> > http://genome.ucsc.edu/cgi-bin/hgCustom >>> > >>> > However, it shows the following webpage. I don't understand what the >>> > problem is. Can somebody help me? >>> > >>> > Error Unrecognized format line 1 of <some web="">>> > link>/NA_MACS_no_track_small.bw: &? ? ?(note: chrom names are case >>> > sensitive) >>> >>> I send the above message with an attachment. But somehow, it is not >>> posted in the mailing list archive. >>> >>> NA_MACS_no_track_small.bw was generated in the following commands. I >>> tried to add the track. But I got the above error message. Can >>> somebody let me know what I was wrong? >>> >>> $ fetchChromSizes mm9 > mm9.chrom.sizes >>> $ wigToBigWig NA_MACS_no_track_small.wig mm9.chrom.sizes >>> NA_MACS_no_track_small.bw >>> $ cat NA_MACS_no_track_small.wig >>> variableStep chrom=chr10 span=10 >>> 3001501 1 >>> 3001511 1 >>> 3001521 1 >>> 3001531 1 >>> 3001541 1 >>> 3001551 1 >>> 3001561 1 >>> 3001571 1 >>> >>> BTW, does this mailing list accept emails with attachments? >>> >>> Regards, >>> Peng >>> >>> _______________________________________________ >>> Genome maillist ?- ?Genome at soe.ucsc.edu >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ > Genome maillist ?- ?Genome at soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome