Hi Yunfei, The browser is able read more than one chromosome at a time as long as lines with the same group are all on the same chromosome and the same strand. The reason for this is that all lines with the same group are linked together into a single item (see field 9 here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#GFF). So, if lines in the same group are on different chromosomes, the browser cannot draw all them as a single linked item. When I entered your data, I got the following error:
Error GFF/GTF group TG2 on chr21-, this line is on chr22-, all group members must be on same seq and strand If I change your data so that items on different chromosomes don't share a group (I just added the chromosome to the end of the group to differentiate it), then it loads without errors: track name=regulatory description="TeleGene(tm) Regulatory Regions" chr21 TeleGene promoter 10010000 10010100 900 + . TG1_chr21 chr21 TeleGene promoter 10020000 10025000 800 - . TG2_chr21 chr22 TeleGene enhancer 10000000 10001000 500 + . TG1_chr22 chr22 TeleGene promoter 10010000 10010100 900 + . TG1_chr22 chr22 TeleGene promoter 10020000 10025000 800 - . TG2_chr22 chr22 TeleGene promoter 10000000 10025000 300 - . TG2_chr22 I hope this is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/10/11 8:58 AM, Yunfei Li wrote: > Hi, > > I try to upload a sorted gff file to genome browser(human), but I keep get > warnings, then I did some test: > 1. I found genome browser will work when gff file is sorted by chrID(first > column) and strand(7th column). > > 2. Does genome browser can only read one chromosome a time? since I found > following 2 example can be read separately but cannot be read if combine > them together > example 1: > > chr21 TeleGene promoter 10010000 10010100 900 > + > . TG1 > > chr21 TeleGene promoter 10020000 10025000 800 > - > . TG2 > example 2: > > chr22 TeleGene enhancer 10000000 10001000 500 > + > . TG1 > > chr22 TeleGene promoter 10010000 10010100 900 > + > . TG1 > > chr22 TeleGene promoter 10020000 10025000 800 > - > . TG2 > > chr22 TeleGene promoter 10000000 10025000 300 > - > . TG2 > > Is my understanding correct? Is there a way that I can upload all my data at > one time? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
