Hello David, We cannot provide advice on scientific direction as to the relative merit of different methods for estimating expression. For your first method, unfortunately we do not offer the raw alignment files for that track for download. If you want them you will have to contact the track contributor directly. You can read more about the contributors in the "Credits" section of the track description page - accessible by clicking on the gray bar to the left of the track in the main display or by clicking on the track title above its pulldown menu.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/9/11 9:22 AM, Managadze, David (NIH/NLM/NCBI) [F] wrote: > Hi, > I have a list of human genes and am trying to estimate their expression in > different tissues using RNA-seq data. > > What would be the easiest and best way to do this? > Would it be to: > 1. get the original alignment files (.bam/.sam) and map them to my genes' > coordinates? > > 2. get the tables from UCSC browser? My guess is that these tables already > contain the info that might be used. In particular, there is "name" field > with ENSEMBL IDs. By simply counting the number of occurance of particular > ENS ID one might get the proxy of expression. > > > I tried to do the first approach. > I found that the track "Burge RNA-seq" contains RNA-seq info for several > tissues, but I could not find corresponding alignment files in ftp. Where are > they? > > I also tried another approach and got some numbers but I am not sure whether > they correlate with the reality or not. > > > Another important point: the approach must be universal, so that one can > easily use it for other organisms. > > Please suggest. > Thanks, > > David > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
