Demultiplex without barcode file

[AndreFC]

Dear All,

Concerning the demultiplex stage I have some questions about the comands input below:

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?

2- What kind of file is the .qza? Is it the folder with the paired sequences? Can I just put the folder with the paired sequences as input?

3- The barcodes file is just an excel one save in .tsv? Do we need to put the barcodes and the samples name? How to transform into .fastq files? I just have them in excell.

I would greatly appreciate for any clarification.

Andre

[thermokarst]

Hi @AndreFC, you need to know what barcodes represent what sample in order to demultiplex. The barcodes do not need to be saved in their own seperate "barcode reads" fastq file. One option is to use q2-cutadapt to demux, check out this tutorial:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin,…

Keep us posted!