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
