Paired-end Cutadapt Produces Empty List

usegalaxy.org support
#1

Using cutadapt with a paired collection produces an accurate cutadapt report, with a full list of adapter sequences trimmed; however, the sequence output is an empty list. I selected “Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)” but still only receive an empty list as the output.

Please note that when using cutadapt with a single read file, the report is generated correctly, and the multiple outputs are generated correctly as a list. Is there an optimal way to specify cutadapt paired read inputs to generate the correct output?

#2

Change your tool and then examine the results.
Recommending Trim Galore or Trimmomatic

#3

Unfortunately TrimGalore and Trimmomatic cannot perform the cutadapt function of separating the reads by internal adapter, while retaining the “untrimmed” sequence. cutadapt can accomplish this function easily in a unix/linux environment, but fails on Galaxy.