Hi Dana, The first three required BED fields are chrom, chromStart, and chromEnd, followed by 9 additional optional fields. Your file is not in the correct format, which is why it's not being recognized. Please see the following page for more details on BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
Contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 4/24/2012 12:53 PM, Levasseur, Dana wrote: > > Hi Luvina, > > Thank you for your quick response to my question. I thought I was > following the .bed format with my data below but I received the > following error message: > > Error File 'AS_transcript_CustomTrack.txt' - Unrecognized format line > 2 of custom track: chr6 + 122673186 122679397 122673401 122679174 4 > 122673186,122677156,122678247,122678760, > 122673552,122677422,122678334,122679397, 0 Nanog cmpl cmpl 0,1,0,0, > (note: chrom names are case sensitive) > > track name="variants" description="alternative splice variants" > color=0,100,0 useScore=0 > > > > > > > > > > > > > > chr6 > > > > + > > > > 122673186 > > > > 122679397 > > > > 122673401 > > > > 122679174 > > > > 4 > > > > 122673186,122677156,122678247,122678760, > > > > 122673552,122677422,122678334,122679397, > > > > 0 > > > > Nanog > > > > cmpl > > > > cmpl > > > > 0,1,0,0, > > chr6 > > > > + > > > > 122673213 > > > > 122680254 > > > > 122673401 > > > > 122679174 > > > > 4 > > > > 122673186,122677156,122678247,122678760, > > > > 122673552,122677422,122678334,122679397, > > > > 0 > > > > Nanoga > > > > cmpl > > > > cmpl > > > > 0,1,0,0, > > Can you tell me what might be the problem by looking at the enclosed > .txt file (coordinates are from mouse mm8 version)? > > Thank you, > > Dana > > ------------------------------------------------------------------------ > > *From:*Luvina Guruvadoo [mailto:[email protected]] > *Sent:* Tuesday, April 24, 2012 2:31 PM > *To:* Levasseur, Dana > *Cc:* '[email protected]' > *Subject:* Re: [Genome] Gene prediction custom track > > Hi Dana, > > Your custom track data should be in a tab-separated file using one of > the formats supported by the Genome Browser. This help page provides a > description of each format: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks. > I suggest using BED format for your purposes. > > I hope this helps. Please contact us again at [email protected] > <mailto:[email protected]> if you have any further questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > On 4/24/2012 9:41 AM, Levasseur, Dana wrote: > > Hello, > > I am trying to upload a custom track to the genome browser that will enable > me to display alternative transcripts. I have downloaded the RefSeq table and > thought I was following the format correctly (below and enclosed) but when I > upload this custom track I receive a formatting error. Ideally, I would like > the track to display formatting identical to that of the RefSeq gene track. > Can anyone assist? > > track name="variants" description="alternative splice variants" color=0,100,0 > useScore=0 > chr6 + 122673186 122679397 122673401 122679174 > 4 122673186,122677156,122678247,122678760, > 122673552,122677422,122678334,122679397, 0 Nanog cmpl > cmpl 0,1,0,0, > chr6 + 122673213 122680254 122673401 122679174 > 4 122673186,122677156,122678247,122678760, > 122673552,122677422,122678334,122679397, 0 Nanoga > cmpl cmpl 0,1,0,0, > > > Dana > > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > > > > _______________________________________________ > Genome maillist [email protected] <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > ------------------------------------------------------------------------ > Notice: This UI Health Care e-mail (including attachments) is covered > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the > intended recipient, you are hereby notified that any retention, > dissemination, distribution, or copying of this communication is > strictly prohibited. Please reply to the sender that you have > received the message in error, then delete it. Thank you. > ------------------------------------------------------------------------ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
