I am new to chip-seq analysis. I am using Bowtie to align one fastQ file to reference genome. Do I do alignment one file at a time or can I run all 9 files at the same time? I found this useful page: http://seqanswers.com/forums/showthread.php?t=14318 but I would like to know where they are actually writing their commands/promts --> terminal in mac?
Any help is greatly appreciated!