trimming fastq files

Question

[gina02]

I have the fastq files of the data I want to trim. In the FastQC I saw that Nextera adapters were present in my sample. I saw few tutorials and it required to copy the sequences to the current directory so this was the command I used cp ~/.miniconda3/pkgs/trimmomatic-0.39-2/share/trimmomatic-0.39-2/adapters/NexteraPE-PE.fa . and the error I got was cp: /Users/ponmalar/.miniconda3/pkgs/trimmomatic-0.39-2/share/trimmomatic-0.39-2/adapters/NexteraPE-PE.fa: No such file or directory

I'm unable to proceed from this, I've just started out and I'm a complete novice in this field.

Answer 1

[Philipp Bayer]

You could download the files from the Trimmomatic repository:

wget https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/NexteraPE-PE.fa