I recently installed the cutadapt with the: pip install --user --upgrade cut adapt I try to run the mode 3 of MaGeCK where I need to trim the 5'adapter seq for the fastq file ERR376998
The problem is that I do get the message:
bash: cutadapt: command not found
,when I try to run the order : cutadapt -g CTTGTGGAAAGGACGAAACACCG -o output.fastq ERR376998.fastq
Any ideas why? Thank you very much!