I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a reference genome. Figured Cuffquant would do the trick, but what to do with the .cxb file that results?? Why not a .csv file, or at least the option to pick up front? Any suggestions anyone?
BTW, it would be lovely if it were possible to access htseq from the Galaxy menu and input BAM files and the gtf and get a raw counts matrix out.