Cutadapt

Question

[Tonyzeng]

Just the first time to use cutadapt today with not bioinformatic background. First, Installment of cutadapt looks work when I input cutadapt command in Linux. However, When I input commands as

$ cutadapt -a ADAPTER-SEQUENCE input.fastq > output.fastq,

How can I put my input.fastq and cutadapt under the same directory to implement command smoothly since I saved the input fastq file on the desktop and cutadapt package under other directory of downloads on my MAC book?

Answer 1

[Devon Ryan]

They don't have to be in the same directory, you simply need to add cutadapt to your $PATH. If you type: echo $PATH from the Terminal, you'll get a list of directories, separated by a ":", that indicate locations to which you can copy the cutadapt executable. Then, you can simply "cd" to the directory with your input fastq file and run the command as you suggested. Alternatively, you could add the directory containing the cutadapt executable to your $PATH, but that's a longer explanation.

You'll be well served to get a book on using OSX or Linux from the command line, since this is a question surrounding basic computer usage.