Trimmomatic Error and Permission Denied

Question

[boydmm6]

I am trying to run a sequencing file through Trimmomatic and each time I try to open the zipped file of Trimmomatic I encounter the error message "permission denied". This is only my second day doing any sort of coding. I am on a Linux. When I downloaded the original Trimmomatic file my understanding is there should have been a trimmomatic.jar file but the only one I have access to is a zipped file. When I extract it it just opens me to the computer's downloads folder. Totally lost. If anyone could help me it would be awesome.

[mastal511]

First, you want to make sure you download the binary version of trimmomatic and not the source version.

Then, from the linux command line, you need to unzip the file with the 'unzip' command. The downloaded file needs to be in a directory where you have write permission in order to modify files.

Hope this helps.

[ATpoint]

As a well-intentioned advice: Spend some quality time on the basics of Unix command line usage and coding, before you dive into productively analyzing whatever data you have. Otherwise, you may waste a lot of time on simple technical problems which in the end keep you from productively working on your scientific question.