Thank you so much! I think this worked, although I'm running into another problem in the next step when I try to demultiplex the reads that makes me think it didn't actually work..
I am using this code:
qiime demux emp-paired
--i-seqs paired_end_seqs.qza
--m-barcodes-file MapingFile.txt
--m-barcodes-column BarcodeSequence
--o-per-sample-sequences demux
--o-error-correction-details error_details
--output-dir demux_dir
--p-rev-comp-mapping-barcodes
and the error message I get is:
Plugin error from demux:
*** Mismatched sequence descriptions: N:0:0, N:0:NGAGTTGTAGCGA, and N:0:NGAGTTGTAGCGA***
Debug info has been saved to /tmp/qiime2-q2cli-err-n3za1s2l.log
I found another thread where N:0:1 did not match and they redownloaded the files and everything worked, but we do not have the original files from the MiSeq, and my issue starts with N:0:0 (Plugin error from demux: Mismatched sequence descriptions). My fastq.gz files still work with Qiime1, but crossing over to Qiime2 seems to be a huge issue...