I'm newbie for metagenome analysis, Qiime2 and have been studying for days. I've searched a lot about DNA barcode sequence but there are several unsolved questions.
- What does exactly DNA barcode sequence mean? As I know, DNA barcode sequences are for species identification so that when their DNA are sequenced, the specific DNA barcode sequences are attached right after the adapter. (5'-Adaptor-barcode sequence-fragment-adaptor-3'). Does this mean all of E.coli's sequenced file(fastq), for example, have same barcode sequence? Then what does the DNA barcode sequence mean used in metagenome sequencing? We don't know what species in sample.
- How do I know whether barcode sequence is in fastq sequence file? Like, when I try to follow metagenome analysis process in dissertation and get data from ncbi, there is no barcode sequence file, only fastq sequence files even though the project is metagenome analysis.
- It could be simple question. When I search for metagenome analysis in ncbi, there are a number of files named similar(e.g Bulk_soil.1, Bulk_soil.2, Bulk_soil.3 .....). What does this mean? Does this mean soil picked different times or location? Since there is no written detail of them.
Actually, barcodes are needed when your running multiple samples in one run of sequencing. These index sequences/barcode sequences used to identify which read is coming from which sample.
Generally, barcode sequences will be in the header of your .fastq file. The last segment of few nucleotides appended to the sequence header will be your barcode for that read. read more from qiimea
It depends on the experimental designing they have done. It could be 3 different places from where they have collected their samples or it could be soil from the same place with 3 different time points, or it could be same soil samples with 3 different treatment.
If I have the data demultiplexed, how can I do my metadata table if it has to have one label called: 'barcode'? Please answer. I will appreciate your answer.
This link from Qiime2 doc should help. There are links for example metadata files if you scroll down on the page.