Hello! My name is Lucia and I’m currently working with already joined reads (qiime2019.1) that I’ve imported as `‘SampleData[JoinedSequencesWithQuality]’ . I’ve checked it and the data still have the primer sequences that should be removed. I’ve tried to use cutadapt using both trim-possible versions (single and paired), but in both cases I obtain the same error regarding the type of argument:
qiime cutadapt trim-single --i-demultiplexed-sequences qscore_joinedF-end-demux.qza --p-front TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNBGCASCAG --p-adapter GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACNVGGGTATCTAATC --o-trimmed-sequences noprimer_qscore_joinedF-end-demux.qza
Plugin error from cutadapt:
Parameter ‘demultiplexed_sequences’ received an argument of type SampleData[JoinedSequencesWithQuality]. An argument of subtype SampleData[SequencesWithQuality] is required.
Is there any option for trimming joined sequences with cutadapt? If not, should I import the sequences as SequencesWithQuality? How does the importation as JoinedSequencesWithQuality or SequencesWithQuality could affect the data? (sorry if this questions does not belong to this chat).
Thank you very much,