Hi Deli, We recommend using bigBed. We have a utility called bedToBigBed which can be used for the conversion. More information on bigBeds and the bedToBigBed utility can be found here:
http://genome.ucsc.edu/goldenPath/help/bigBed.html If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Deli Liu <[email protected]> Date: Tue, Dec 20, 2011 at 8:34 AM Subject: Re: [Genome] xenoRefGene Help To: [email protected] Hi I am trying to upload RNA-seq results into the UCSC genome browser in http://www.genome.ucsc.edu/cgi-bin/hgCustom. And I make my input format same as * *ENCODE RNA elements: BED6 + 3 scores format, but I still cannot upload the data by specifying the track type: # Displaying first 50 lines of data track type='BED6+3' chr1 3241624 3242705 CUFF.1.1 1000 + 1.1704528930 0.05 2.552442 chr1 3243860 3244536 CUFF.2.1 1000 + 1.2850250455 0.05 2.714722 chr1 3363571 3363757 CUFF.3.1 1000 + 19.6351241782 0.05 23.244555 chr1 3363904 3363988 CUFF.4.1 1000 + 719.2170299779 0.05 784.209311 It seems I have the problem in the track type. So which track type I should use to upload my RNA-seq results with fpkm value and reads density? Thanks a lot. Best On Wed, Jun 29, 2011 at 4:00 PM, Deli Liu <[email protected]> wrote: > What does exonFrames (-1, 1, 0, 1 and 2 in last column) mean in the > xenoRefGene of dog canFam2? > > NM_020923 chr37 + 17871328 17896391 17880435 17893285 40 > 17871328,17880435,17886560,17887180,17887966,17888306,17888578,17888815,17889124,17889261,17889288,1 > > 7889647,17889913,17890291,17891753,17892167,17892439,17892654,17893060,17893874,17894018,17894082,17894182,17894353,17894462,17894608,17894762,17894806,17894 > 847,17894887,17894948,17895118,17895149,17895258,17895360,17895416,17895514,17895853,17895939,17896032, > 17871373,17880582,17887158,17887943,17888209,17888567 > > ,17888806,17889111,17889131,17889277,17889396,17889677,17890274,17891509,17892139,17892286,17892571,17892687,17893285,17893966,17894044,17894099,17894191,178 > 94403,17894576,17894662,17894780,17894825,17894873,17894902,17895041,17895136,17895238,17895321,17895396,17895467,17895554,17895898,17896023,17896391, > 0 ZDBF > 2 incmpl incmpl > -1,1,1,0,0,1,0,0,0,2,2,1,0,0,1,1,0,2,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, > > Thanks a lot > > -- > Deli Liu > Institute of Bioinformatics, University of Georgia > Athens, GA, 30605 > -- Deli Liu Institute of Bioinformatics, University of Georgia Athens, GA, 30605 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
