When demux performs golay error correction, it outputs a file with “Detail about the barcode error corrections.” This file is specified with
--o-error-correction-details. My question is, how do I view the error correction details? Or, if this is not something that is visualized, what is the file format?
Example demux command:
# perform demux using golay error correction $ qiime demux emp-paired --i-seqs data.qza --m-barcodes-file barcodes.txt --m-barcodes-column BarcodeSequence --o-per-sample-sequences data_golay.qza --p-golay-error-correction --o-error-correction-details data_golay_errors --p-rev-comp-barcodes --p-rev-comp-mapping-barcodes Saved SampleData[PairedEndSequencesWithQuality] to: data_golay.qza Saved ErrorCorrectionDetails to: data_golay_errors.qza
I thought maybe the output would be the sequences that were thrown out or corrected, but it doesn’t look like it is formatted as fastq files anymore:
# try to visualize it the same way as the other demux output: $ qiime demux summarize --i-data p1_golay_errors.qza --o-visualization p1_golay_errors ... There was a problem with the command: (1/1) Invalid value for "--i-data": Expected an artifact of at least type SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]. An artifact of type ErrorCorrectionDetails was provided.
Since I still don’t know what “type ErrorCorrectionDetails” is, I tried drag and dropping it into the qiime object viewer: https://view.qiime2.org
But this also just tells me that the file is:
Thanks for your help understanding what this file type is!
(qiime2 Version q2cli 2019.4.0 in conda on mac)