Hello, Alignment data can be adding as a custom track two ways:
1) Run a blat and select "custom track" as an output option 2) Format your alignment data to be one of the formats accepted by the Custom track tool. As long as your data is aligned to the version of the genome that you want to view it against, both of these will work. Your question was slightly difficult to understand - is your concern that the data will be multiple sequences deep at any particular genomic location? If so, that should not be a problem. If I have misunderstood your question, please send more detail. Links to Custom track help: http://genome.ucsc.edu/goldenPath/help/customTrack.html Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Li, Zhihua wrote: > Hi netters, > > I was wondering if there's way to show the mapping of RNAs to the genome as > multiple alignments in a custom track. > After large-scale sequencing, people always map tons of sequenced RNAs to the > genome. Because lots of sequence variants can be mapped > to the same genomic region, you actually get a lot of multiple alignments in > segments of the genome. It's easy to show the mapping coordinates > , but I don't see a way to actually show the alignments. > > I noticed that UCSC has a MAF format by which you can show multiple genome > alignment in a custom track. But my RNA mapping alignments > are different in that RNAs are not coming from other genomes, and different > blocks may have different number of aligned sequences. > > Is there some way to show these kind of alignment in a custom track? > > Thanks a lot! > > > Sincerely Yours: Zhihua Li > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
