@TonyBolger I am creating a pipeline with Trimmomatic being our tool of choice for adapter trimming. One issue in practice is that it's hard for analysts to figure out the correct adapter sequence to use. For that reason, many would turn to Trim Galore instead where adapter can be auto-detected if not specified.
is there a way I can still use Trimmomatic without having to specify the adapter file -- either that trimmomatic can detect it, or, if there are auxiliary codes you could point to me so I can use that to generate the adapter file for input to Trimmomatic? Thank you!
@TonyBolger I am creating a pipeline with Trimmomatic being our tool of choice for adapter trimming. One issue in practice is that it's hard for analysts to figure out the correct adapter sequence to use. For that reason, many would turn to Trim Galore instead where adapter can be auto-detected if not specified.
is there a way I can still use Trimmomatic without having to specify the adapter file -- either that trimmomatic can detect it, or, if there are auxiliary codes you could point to me so I can use that to generate the adapter file for input to Trimmomatic? Thank you!