[galaxy-dev] TopHat paired end

Hello,

I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse).

I want to analyze the data in Galaxy.

Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample.

Ultimately, How do I run TopHat for paired-end data. When I select paired end data in Galaxy, it gives an option to upload both files should I upload both forward files once and reverse files once. Or should I combine both the files before running the TopHat.

I am all confused. Any kind of help will be appreciated

Thanks in advance