I did the demultiplexing. The company provides a FastQ processor which somes with the next description: " files generated from Illumina NGS platforms and creates a directory containing fastq files for each individual sample. The input files required by the user are the unzipped RAW Read 1 and Read 2 fastq files as well as the corresponding mapping file. The output directory will contain a new Read 1 and Read 2 fastq file for each sampleID as well an additional directory containing the index file. This tool was created in order to assist users who are interested in using mothur or qiime in order to process their 16s rRNA gene sequences This tool was created in order to assist users who are interested in using mothur in order to process their 16s rRNA gene sequences. The output directory can be referenced by the mothur make.file command, which will generate the necessary files to proceed with the mothur MiSeq workflow. The necessary index and oligos file are also provided should you choose to not to use the mothur make.file command."
Also, I have already ran DADA2 on my samples, after processing i lost around 20,000-30,000 reads per sampl. Also, the sequences still have the primers so thats why i used dada2 to remove the. Can you trim the 5’ with deblur too?
And I´m going to write them asking more info about their process. Thanks for the suggestion!
EDIT: just checked the pipeline and there wasnt anything strange about the sequencing process, the files are fully raw and unbinned. So I guess my samples are a rare case.
Another Edit, looking around the forum I noticed this post Importing and Demultiplex process for 4 Fastq Files: R1, R2, Index1 and Index2 in which her data comes with R1, R2, index1 and index2 files to import into qiime2. I think I did Import the data wrong (Because I used the Casava1.8 instead because the files looked like the ones that you can import with this method) but checking my separated R1 and R2 files seems there isnt a barcode in the sequences.