I am rerunning a project through QIIME2 that was originally ran using QIIME1 about two years ago.
The sequences files are all combined and there are a couple of samples that share barcodes. The person who ran the project in QIIME1 was somehow able to deal with the duplicate barcodes, but did not leave any documentation regarding how they split the files or even leaving the split files. I’m having to try to figure out how to split the files and import them into QIIME2.
I have tried splitting the files using QIIME1 and then importing and demultiplexing them only to have three samples with a count 1 output according to the qzv file.
Here are the commands I ran on the first set of samples that I split from the original fastq file.
extract_barcodes.py \ -f split_libraries_fastq_processedseqs_set_1/seqs.fastq \ -c barcode_single_end \ --bc1_len 8 \ -o processed_seqs_set_1/ gzip processed_seqs_set_1/barcodes.fastq gzip processed_seqs_set_1/reads.fastq qiime tools import \ --type EMPSingleEndSequences \ --input-path processed_seqs_set_1/ \ --output-path qiime2/sequences-set-1.qza qiime demux emp-single \ --i-seqs qiime2/sequences-set-1.qza \ --m-barcodes-file 051116JS515F-mapping2-set-1.txt \ --m-barcodes-column BarcodeSequence \ --o-per-sample-sequences qiime2/demultiplexed-seqs-set-1.qza qiime demux summarize \ --i-data qiime2/demultiplexed-seqs-set-1.qza \ --o-visualization qiime2/demultiplexed-seqs-set-1.qzv
Thanks in advance