Hi Again, Yes, it is microarray data. Sorry I forgot to mention that.
I have been browsing through all the documentation I can find online and in the source tree, and checked the sample .ra files (and the microarrayGroups.ra file). I have tried to use the fields 'expDrawExons off', and the 'exonArrows on' in my track stanza (and of course reloading the file to the db), but I have had no success so far in hiding or changing the appearance of the probe on the browser. We would also like to be able to display all samples belonging to a specific subset of the total set of samples (cell-lines, lymphoma samples etc.), but it seems that the subset-display-functionality, which is also used in the affyHumanExonGroups in the microarrayGroups.ra file is broken somehow. I can't make it work with our own data, nor with the affyHumanExon (Affymetrix All Exon Chips) data. Has that feature been removed from the browser? I think that the documentation is somewhat 'fuzzy' about that. It is not specifically mentioned in the microarrayGroups.ra-WIKI (http://genomewiki.ucsc.edu/index.php/Microarray_track), but the affuHumanExonGroups stanzas are still mentioned as a sample, with a reference to the subset stanzas affyHumanExonSubsetByTissue and affyHumanExonSubsetByReplicate even thought neither of the referenced stanzas are shown - it's a bit confusing... Kind Regards - Frank Hi Frank, From your image, it looks like you may not be using all the fields available for microarray custom tracks (which is what I think is being shown in your image). If you want to show boxes with a thin line connecting between them for the probes spanning splice sites, it is possible with the microarray format. For more information, please see this FAQ:http://genome.ucsc.edu/FAQ/FAQformat.html#format6.5 I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Frank Sørensen wrote, On 03/04/11 05:36: > > Hi, > > > > Is there any way to make the browser visualise probes that span > > splice-regions as two separate sections instead of just a big one? > > > > Regards > > > > - Frank > > > > i.e. the green bars in this screen dump. > > > > > > > > -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. 8949 9463 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
