Tophat 2.0.2 on multiple Single-End reads: need som help

[sindrle]

Hi!
So, I have now 2 or 3 .fastq files from each sample (50 samples in total, but <150 fastq files). What does that mean?
Its single-end reads btw.

I want to run tophat2 on these files, should I merge them somehow or can tophat2 run them all at the same time?

Thanks!

[GenoMax]

An aside on merging data : http://seqanswers.com/forums/showthread.php?p=100078

TopHat2 can accept multiple files separated by a comma (http://tophat.cbcb.umd.edu/manual.shtml#toph)

2.0.10 is the latest version. Is there a reason you want to run 2.0.2?

[sindrle]

Thank you!

We have an earlier run on other tissues, using 2.0.2. For comparable results we have chosen this old version. Or, more correctly, my supervisor has instructed me to do so...