Hello, I have successfully installed tophat2 with bowtie2 and samtools and have created my bowtie2 indices. I have paired end reads for several different conditions. My questions: 1. Is it possible to run these different sets in separate terminals simultaneously?
The default output directory is tophat_out. How can I determine a separate output directory for each data set? I tried using the -o/ or --output-dir command given in the tophat manual but its not working.
As I am new to tophat, What is the best approach for mapping, the above method or giving all different sets in a single command line (wouldn't the output be confusing)?