Hi Eric, Note that the BAM format was created by SAM tools, not UCSC, so if you need additional info, please trying their help list: https://lists.sourceforge.net/lists/listinfo/samtools-help
One of our engineers commented: "Short answer: the user needs to set bamColorTag to "YC" not "YC:Z:247,251,255" which is the format that should appear in data lines in the SAM/BAM file. The SAM spec used to mention 'Y?' in addition to 'X?' as a pattern for user-defined tags, but I see the current http://samtools.sourceforge.net/SAM1.pdf 's second table in section 1.5 just has 'X?'... bummer. Section 1.5 begins: "All optional fi elds follow the TAG:TYPE:VALUE format where TAG is a two-character string that matches /[A-Za-z][A-Za-z0-9]/." The code is expecting a TAG (not TAG:TYPE:VALUE as user is trying) and the error message kind of paraphrases the spec's regular expression... Not that the error message is clear or anything! I guess we could add a reference to the spec's section 1.5 in the error message, but http://samtools.sourceforge.net/SAM1.pdf is subject to change." Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 1/8/12 9:36 AM, Eric Guo wrote: > Hi there, > > > I have trouble using R,G,B colors to specify user-defined tags. When I > configure my custom track, I always get the following error message: > > > Error: > > * B+D.bam: BAM tag 'YC:Z:247,251,255' is not valid -- must be a letter > followed by a letter or number. > A quick search in the mailing list archives did not give any results. Does > anyone know what is wrong? How can I color my tracks? > > Thanks in advance for your help. > > -Eric > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
