Demultiplex - No barcodes and Forward Reads

[AndreFC]

Dear All,

I am having some issues during the demultiplex stage:

qiime demux emp-single
–i-seqs emp-single-end-sequences.qza
–m-barcodes-file sample-metadata.tsv
–m-barcodes-column BarcodeSequence
–o-per-sample-sequences demux.qza
–o-error-correction-details demux-details.qza

Q1- Is there any method to demultiplex without associate to barcode (In Qiime 1.9.0 I used the multiple_split_libraries_fastq.py –i folderpairedsequence –o outputfolder –demultiplexing-method sampleid-by-file? Is there any similar command like this one in QIIME 2?
I have a folder with the paired files and another with the Mapping File (Metadata).
How can I do the demultiplex without the metadata and barcode files, like this command in QIIME 1.9.2 multiple_split_libraries_fastq.py?

I would greatly appreciate for any clarification.

Andre

[colinbrislawn (Colin J Brislawn)]

Hello Andre,

Good afternoon.

Yes! Check out the import guide for the fastq manifest format, as it works a lot like the multiple_split_libraries_fastq.py script and gives you even more control over sample names.

Let us know if you have any questions!

Colin

[AndreFC]

Dear Colin,

In this case what would be the similar command in QIIME 2 for the case below?
multiple_split_libraries_fastq.py –i folderpairedsequence –o outputfolder –demultiplexing-method sampleid-by-file

[colinbrislawn (Colin J Brislawn)]

Yes! The command would be something like

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path pe-33-manifest.tsv \
  --output-path paired-end-demux.qza \
  --input-format PairedEndFastqManifestPhred33V2

Note that instead of passing a folder, like folderpairedsequence, you list the files in that folder inside of the pe-33-manifest.tsv file.

(All the details are in the folder I linked to above )

Colin