I am a new postdoc student and I was given a folder of fastq.gz files. I was told they are not de-multiplexed and I need to basically extract each sample information separately from each of these fastq file (they contain info for multiple subjects) and save it as fastq file and run dada2 pipeline on them to get ASVs. My apologies if I am not using some terms correctly, I am very new to this. I worked with ASV table before, but never done de-multiplixing before. If you can help me how to do it or what software or platform I can use to separate these samples, I appreciate your help.
You typically demultiplex Illumina sequencing data with the program
bcl2fastq. As the name implies, it converts the original basecall files (.bcl) from the sequencer into the demultiplexed .fastq.gz output directly. This is done with a .csv formatted samplesheet. Your best bet is to figure out who did the sequencing and get them to demultiplex it. This is typically done automatically by the sequencing facility. Trying to demultiplex it after the fact is kind of a waste of time because it will be much harder and slower.