I'm currently using the CutAdapt tool on Galaxy to remove adapter sequences from fastq-format data.
Because my dataset is sizable, I find that it would be needlessly time-consuming to process each input in the dataset individually.
Fortunately, CutAdapt has a batch mode that allows for operative trimming on multiple data in the dataset at the same time.
However, I'm out of depth as far as entering 3' and 5' adapter input when processing data in batch mode. Any pointers, guys? Thanks.