Hi, how do you map reads using TopHat when you have several replicates? Does it work like this:

```
tophat -p 8 -o output_dir \
  ./path_to_bowtieindex \
  ./path_to_replicate1 \
  ./path_to_replicate2 \
  ./path_to_replicate3
```

I am omitting most of parameters I use to keep it short.
<p>Technical or biological replicates? What you showed will work for the former, but not the latter. For the latter, you need individual runs of tophat, since you need the output in different files.</p>
