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
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