You may also find these UCSC Browser help pages useful: http://genome.ucsc.edu/goldenPath/help/bam.html http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html
On 1/9/12 3:45 PM, Greg Roe wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
