Hi Colin, If you are using GFF (or GTF) format, note that this format relies on transcript name to join separate exon coordinates; the same transcript name can't be used more that once in the same file. One of our engineers suggests two possible solutions for this:
1. Translate each GFF file into BED, which supports multiple transcripts having the same name. Then concatenate the pre-transcript BED files into a single BED files to use as a custom track. 2. Add a unique suffix to each transcript name, so files can be concatenated into a single custom track. E.g. if there are 3 transcripts of MYGENE, before concatenation, change the transcript names to MYGENE_1 from the first file, MYGENE_2 from the second file, and MYGENE_3 from the third file. I hope this information is useful and resolves the issue. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 7/5/2012 10:20 AM, Colin Shaw wrote: > Hello, > I'm having trouble compressing/hiding tracks in the Genome Browser. I have > uploaded a bunch of custom tracks and I was wondering if there is a way to > maintain the descriptors that are present when each gene (in this case) is > uploaded as its own track i.e. name, NM_##, etc, while putting all the genes > into one transcript. The solution would allow multiple transcripts for a > gene in a single track. I am looking for a solution similar to what > appears in the Browser when you go to a gene's location. For example, when > FGFR is entered, there are 9 transcripts, which are shown in the window, but > the lines (on the left bar in the browser) for other genes are hidden i.e. > there are not 3 lines reserved for EGFR. In short, what I'm asking is this: > how can I show only the transcripts that are currently in the viewing window, > without having to click "hide" and "dense" whenever I switch between genes? > A copy of my session can be found here. > > Thanks in advance, > Colin > > Colin Shaw > [email protected] > (404) 983-2882 (m) > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
