I'm helping a student with a human bioinformatics project. We would like to generate a single relative gene expression value for each gene in the human genome (for different cell lines of interest) using the RNA-seq data from the UCSC archive. We can see raw signal values by displaying the following file as a track in the Genome Browser:

Track name: BJ cell pA+ + 1
Table name: wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1
File name: /gbdb/hg19/bbi/wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1.bigWig

But where we get stuck is trying to import the wig into Galaxy to generate expression values for each gene. Cufflinks seems like the right tool for the output we want, but we're not sure what the inputs are supposed to be. We'd appreciate any help you can provide.