Primer FileΒΆ
You can set the primer file and the the primer options in the config.yaml file. You’ll want to change the fields under trim_reads. To learn more about the options, see the help fields below, and see the documentation at http://www.usadellab.org/cms/?page=trimmomatic
trim_reads:
primerfile:
default:
help: 'Primer File'
primerseed:
default: 2
help: 'seed mismatches'
palindromeclip:
default: 30
help: 'palindrome clip threshold'
simpleclip:
default: 20
help: 'simple clip threshold'
The available options are:
primerfile: path to the primer file
primerseed: seed mismatches
palindromeclip: palindrome clip threshold
simpleclip: simple clip threshold