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. ________________________________
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,
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