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• Don't forget: it's q() to quit.
• For help, type ?command. Try ?read.table. The q key gets you out of help, just like for a man page.
• The left arrow \<- (less-than-dash) is the same as an equals sign \=.

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For RNA-seq analysis we're mainly counting the reads that align well, so we choose to use bowtie. (You could also use BWA or many other mappers.).

We've done this several times before, so you should be able to come up with the full command lines if you refer back to the original lesson. You will need to first build the index file, just once and in "interactive mode" is fine. Then, you will need to submit a commands file with four lines to the TACC queue.

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