Hi Elane, You can display your data with the height of the item corresponding to the number of reads by converting your data into bedGraph format. Basically, just remove the name and strand columns (4th and 6th columns) from your data:
chr2 145103508 145103534 1 chr2 145107027 145107054 1 chr2 145176537 145176567 1 chr2 145184073 145184097 6 See here for more detailed information about bedGraph format custom tracks: http://genome.ucsc.edu/goldenPath/help/bedgraph.html Alternatively, if you want to keep the name and strand as part of your data (BED format), you can leave all the columns and convert your "number of reads" column to corresponding scores between 1 and 1000 (if your reads already span that range, then no need to change them). In your track line, include "useScore=1" and your data will be displayed in shades of gray based on the score. chr2 145103508 145103534 ch9.fa_11992841 100 + chr2 145107027 145107054 ch9.fa_3807570 100 + chr2 145176537 145176567 ch9.fa_9934488 100 + chr2 145184073 145184097 ch9.fa_5067346 600 + See here for more detailed information about BED format data and the useScore option: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED For more information on creating custom tracks in general see: http://genome.ucsc.edu/goldenPath/help/customTrack.html Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Elane Fishilevich wrote, On 12/02/10 20:53: > Hi, > > > > I would like to display short-read sequencing data in a custom track and > include the number of reads (column 5 in example below) as the height of the > bar; how do I do that? If I cannot alter the height, what are the ways to > represent single versus multiple reads? > > > > chr2 145103508 145103534 ch9.fa_11992841 1 + > > chr2 145107027 145107054 ch9.fa_3807570 1 + > > chr2 145176537 145176567 ch9.fa_9934488 1 + > > chr2 145184073 145184097 ch9.fa_5067346 6 + > > > > Thanks, > > Elane > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
