Hello, Chris. I loaded your sample data as a custom track and experienced the same issue you reported. This appears to be a bug. Thank you for bringing this to our attention. One of our developers will look into this issue.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Davies, Christopher Sent: Tuesday, March 27, 2012 6:45 PM To: '[email protected]' Subject: [Genome] Zero-length items in custom track generating errors Hi All, I'm having an issue in the UCSC Browser with my custom bed files, that I don't think I've seen before.... (Human, hg19, Firefox) If I upload this file: (Or paste it into the browser .... you'll need to convert the spaces back to tabs) track name=test3 description=test3 chr1 111739765 111739766 AX-11111111_T/G_trueSNP chr1 111739771 111739771 AX-83064695_-/CAGGACAAA_deletion chr1 111739775 111739778 AX-33333333_-/CCC_insertion chr1 111739780 111739781 AX-44444444_-/A-insertion All the snps appear normal in the browser, (and have the right length, including an inter-base tick mark for AX-83064695) BUT (e.g. in 'pack' mode) when I click on the ID of the snp AX-83064695 it get the following error message: "Couldn't find AX-83064695_-/CAGGACAAA_deletion@chr1:111739771 in ../trash/ct/ct_genome_4f0d_e3c30.bed" The other snps work fine. This happens only for zero-length snps (all of them!), i.e. where hg19 has the deletion allele. (i.e they map to the inter-base location, so the start and stop are the same integer). Note that in the dbSNP153 track, at this location, rs3833538 displays just fine as an inter-base 'tick' mark, and it's details link is also functional. If I use 9-column format, so that I can use the itemRgb, then it gets weirder. Example: track name=temp4 description=temp4 itemRgb=On chr1 111739771 111739771 AX-83064695_-/CAGGACAAA 0 + 111739771 111739771 0,0,0 Now the interbase tick-mark is not even displayed in the browser. If I use 'pack' mode, then I can see the annotation, but not the tick-mark. If I click on the annotation, I get the same (above) error message. Is this a (new?) bug, or am I now doing something wrong? This used to work for me, I swear... Thanks! -chris davies _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
